Omnipro security recommendation in garage


I've had an omnipro II for a few years used exclusively for security and it works, but not 100%.  This summer I'd like to get working to 100% and then expand into some automation and wireless stuff with Homeseer.  Ideally, for the problems below I'd like to stick with wired solutions with the omnipro, and only do wireless and non-security stuff with Homeseer.
Omnipro II
Zone 1 = front door
Zone 2 = north side windows (~10 in series)
Zone 3 = south side windows (~10 in series)
Zone 4 = exterior garage doors (3 in series)
Zone 5 = basement glass break sensor
Zone 6 = water sensor
Zone 7 = water sensor
Zone 8 = free
Zone 9 = water sensor
Zone 10 = back door
Zone 11 = water sensor
My first and most important issue is Zone 4, the garage doors.  Is it best practice to have magnetic sensors on exterior garage doors, or should I be using a contact sensor on the interior garage door or a motion sensor or something?  My problem is that every few months Zone 4 will trigger for no reason.  How can I get to the root cause of this?  I'm not even sure which of the 3 doors is the issue since they are in series.  I'm also happy to leave the exterior doors as warnings if best practice is to use the interior garage door.  But then I have to add that component.
My second problem is that Zone 3 doesn't work.  I'm not even 100% sure it is the window wiring since it has never worked (i.e. signaled open or closed).  My windows have contact sensors embedded in them.  How can I figure out where the problem is?  I've traced network cable but how can I trace this?
My third problem is Zone 11... or any zone I connect last.  Once I connect power to it, omnipro sends an error/alert.  Am I overloading the system? 
Lastly, one of my door sensor only triggers when it is open about 45 degrees... more than enough to slip through.  Anyway I can reduce that?  It is embedded on the hinge side of the door.
Thanks for any help and advice!
For the garage sensor, I suggest that you inspect all of the sensors.   Check the distance between the sensor and the magnet.   Check all of the connections.   Wiggle each sensor to see if it will alarm.
For the windows, that is a tough one.   First, check the resistance on the circuit with an ohm meter.   Is it shorted, open, or some other resistance?    I have sometimes been successful at (very carefully) pulling each sensor out of the wall and checking the connections.   A Fluke TS90 could help you identify the distance to the fault.   You have to know how the wire is routed for this device to be helpful.   If you can find the wires in the attic, you may be able to cut and isolate the fault.   Otherwise, you could convert to wireless.
Need to know what kind of error you are getting on zone 11.     What type of water sensors are you using, and how much current do they draw?
To fix the door sensor, you need to (very carefully) remove the door casing and re-route the sensor wires top side of the casing.   Install a magnetic sensor in the door casing and a magnet on the top of the door.   It is a hassle because it requires re caulking and re painting the door casing
Last December I added zones to my panel so I could get rid of multiple sensors on a single circuit.  I found only two cases where the builder put two windows on a circuit back to the panel.  Otherwise, all wiring ran to the panel directly.  This allowed me to have almost every door or window on its own zone.  I have two garage doors that also have a sensor on them wired to the panel.
While it might be some work, you might think about adding zones to your panel and breaking everything out.  This also helps troubleshooting if/when you have an issue.
Good point.   It will be much easier to troubleshoot if the system is home runned with all circuits going back to the panel.
The OP at least has zones somewhat organized.  In my case, the original panel as an NX-6V2 and they had 29 doors/windows on 6 zones.  I tried adding a 16 port zone expander and the NX-6V2 would only allow 8 zones to be added; so I had to replace the panel.  Now all that are combined are:
In the garage there are three windows; they are on zone zone as they are in series with one home run back to the panel.
In breakfast nook there are four windows; they are in sets of two since there is only two home runs back to the panel.
In the office there are three windows; the are in series with a single home run back to the panel.
Before if a zone was in alarm, it could be any number of doors or windows.  So you basically had to go to everything to check it.  Now it is far easier as it gets down to only one window or door are at most three windows (but all in the same room.)  It also makes integration into the HA system easier since it knows exactly what is open or closed.
I guess it also depends on how the OP has theirs in series.  In my case, the cables came back to the panel so the installer just put them in series there with the exception of the three listed above.
Another idea for the OP is what I'm also contemplating of doing, which is to put the zone expander module closer to the sensors.  This way not as many wires need to go back to the panel.  I'm also going to put some more heat detectors in the attic and would need to add another zone expander anyway.
What are the zone loop readings on the troubled zones?
I'd disconnect the zone wiring from the panel and do a continuity check, then measure the resistance on the loop.
Do you have EOL resistors enabled?  If yes, are they installed correctly?
Then, keep the multimeter connected and open each window in turn to make sure the individual switches are working correctly.
Make sure continuity is properly broken.  Close the window before moving to the next.  Check the resistance returns to the original value.
If you don't have continuity on the loop you are going to have to trace it window by window until you find the break.
Could be a malfunctioning switch, could be a break in the wiring (got hit by a screw or nail for example).
Zone 3 sounds like a continutiy issue, like you have a break or open circuit somewhere.
For garages (Zone 4) there are special magnetic large gap sensors.  Do you have them?
Intermittent trouble sounds like a bad/poorly crimped connection.
I'd replace each of the crimps with a new and proeprly crimped connector just to rule that out.
Thanks all for the input to my post.  Regrettably, I wasn't able to work on my system the last 5 months due personal reasons, but I'm back at it now with some answers and more questions for any help still out there.
Problem 1- Garage: I can significantly push and pull on the garage doors and can't set them off.  However, a non-windy night recently just set it off.  So I'm thinking it isn't the magnetic distance. As for the setup, only one home run so putting them each on a zone would be a huge hassle.  Regardless, now my wife doesn't trust them (after getting awoken by the alarm while I was traveling and walking the house with a knife)!  So I'm back to my original question, what is best practice?  Should I switch to motion sensor in the garage?  Door sensor on the door between house and garage?  Motion sensor inside on the door to the garage? If motion sensor, is there a recommended wired version?  If the best is a door sensor, will I run into issues since this is a fire door (metal)?
Problem 2- Windows: I'm still working on that
Problem 3- Zone 11: Connecting the water sensor triggers omnipro error "Fuse Had Trouble".  the water sensor is a GRI 2600.
Thanks for the help!
For the garage door zone, use a multimeter to check the loop resistance to see if it might be marginal.   If it is ok, and still gives trouble, you could add a motion detector and either abandon the magnetic contacts, or use both in a cross-zone configuration, so that an alarm will be triggered only if both zones trigger.  That would require new zone wiring for the motion detector.
The FUSE HAD TRBL message means you are overloading the aux power outputs of the panel.  What other loads do you have on the panel?  The GRI 2600 only needs about 12mA, so if you have no other loads, or are below the 1A power limits, it's possible that you have a short in your wiring to the 2600.  Should be easy to check with an ohm meter.
For the window loop, check the continuity of the loop with an ohm meter.  If it is open, you may be able to narrow down where the problem is with a wire tracer, like a Fluke Pro3000.   Disconnect both zone wires from the panel, and connect the signal generator to one of the wires, with the other side of the generator going to earth ground. Then use the probe and go from window to window and see if you can pick up the signal.  If you find a window with no signal, then you know the problem is between that window and the last window with a signal. You might even be able to narrow it down more than that if you can follow the routing of the wires.   Then switch the signal generator to the other wire of the zone and try again.
I gave up on the garage bay doors.  I replaced some of the connections, but then last night it triggered the alarm again at 2 in the morning and my wife was not happy :(
So I've disconnected zone 4 for now, the exterior garage doors.  I'll have to switch to the motion sensors or interior garage door as suggested.
As for "FUSE HAD TRBL" when I connect my GRI 2600, that's the 4th water sensor.  With 3 of them connected I'm fine, but not the 4th.  I also have a glass break sensor (looks like honeywell FG-1625, but I'm not positive).  Other than that, just the horn is connected.
Regarding the windows, thanks, I've borrowed a wire tracer and will try to check that next.
Regarding the power, the keypad bus also counts towards the 1A. How many keypads, wireless receivers, hardwired expanders, etc. do you have on the Omni?
Other than that, just the horn is connected.
I had issues with the very first monitored external horn I used with "FUSE HAD TRBL" errors.
Thinking I posted here way long time ago about the issue.
OmniPro II Random Resets