2003 civic, avital 4103, multiple problems

Due to the intermittent nature of the problem (seems to always be after I give the car back to her), I'm not sure disconnecting the power to the RS will give me a definitive answer. I can only have the car a day or 2 at a time, and the issues never seem to come up when I have the car. So, let me give the detailed wire connection list a go, and you tell me if you see any problems. Not sure I'm doing this in a way that's easy to read, but here goes. Car Wire - Avital Wiring +12v Ignition Harness (white) - Both red high current 12v inputs Starter (Bl/Wh) - Purple output to starter circuit Ignition (Bl/Ylw) - Pink ignition circuit Accessory (Bl/Red) - Orange output to accessory circuit 2nd Accessory (Wh/Red) - Pink/White flex output, programmed to accessory Power Lock (Wh/Blue) - Green lock output Power Unlock (Wh/Grn) - Blue unlock output Brake Wire (Wh/Blk) - Brown brake switch shutdown wire Installed hood pin - Gray hood pinswitch shutdown wire Horn Trigger (Or) - Brown horn output wire Neutral safety switch input on Avital (Bl/Wh) is wired through switch directly to ground (body bolt on car). (car already has factory starter lock-out, incidentally what seems to be my problem). I used this same ground for the black Avital ground. Anti-grind Relay Wiring 86 - Bl/Wh Starter wire from car, key side 85 - Orange GWL output from Avital, programmed to anti-grind ON 30 - Bl/Wh Starter wire starter side and Purple starter wire from      Avital 87a - Bl/Wh starter wire from car, key side 86 and 85 are diode protected, with stripe towards 86 Trunk Release Relay Wiring 86 - +12v constant fused at 5a 85 - RED / Wh trunk release output on Avital 30 - to grounded trunk solenoid 87 - +12v, fused 10a (can't remember right now where I pulled this +12v from) Fortin SL-3 Wiring Blue Status output on Avital to Blue GWR on Fortin RED / Blue on car to PURPLE / White on Fortin Blue/Orange on car cut, Or/Bl on Fortin to key side and Or to vehicle side Yellow/Black on car to Yellow on Fortin White on car to Red +12v on Fortin Br/Ylw on car to Black - on Fortin I'm thinking my problem lies somewhere in my relay wiring, but I'm not sure where. Everything works exactly as it's supposed to, until these crazy intermittent issues. And at this point, I'm worried about causing actual considerable damage to the transmission, given the latest issue.

Update We put a new battery in the car, after finding the old one to be shot. Initially, I thought this had solved all the problems, as everything was fine for a solid month. Unfortunately, twice within the last 2 weeks she's having the issue with the D4 light blinking again, after using remote start. Just by way of refreshing...........she starts the car remotely, then when she puts the key in the ignition and turns to "run" position, the D4 light starts blinking, and the car does a terrible job at shifting. If she shuts the car off at this point, and tries to start with the key it won't crank. Last time around, she was able to turn the car off and leave it for ~10 mins, at which time it started fine. This most recent time, even after 10 mins she had the D4 light problem. Has ANYONE run into this? Is there a stray voltage somewhere that's causing the PCM to think it's in 2 gears at once? Can someone PLEASE help me fix this? I've never been more frustrated with a car problem in my life. And it's made worse by the fact it's always when she's trying to get to work, on the other side of town and it's frustrating her to no end as well.