Over the past month I've been fighting with my megasquirt(MS1 v3). After a bunch of research I've come up with some mods that made my system much more stable and robust.
First problem, I had some massive noise on the +12v line because I'm running low-Z injectors with PWM. Installs with high-Z injectors can see similar problems, but generally not as bad. Most of the noise comes from the flyback circuit. Here's how I remedied it:
1) lift the center leg of both of the flyback TIP125's
2) Solder a wire between them and to one of your spare ports on the DB36, I used one of the IAC ports because I'm not using it and my harness already had a wire there
3)Run a wire from the DB36 directly to your +12v feed to the injectors
I also put a 47uF cap across the center legs of the TIP125's and TIP42's, negative side to the TIP42. I also put a 1uF cap across the boot loader pins. I'd consider this optional, I did this before the other step and left them there after. They helped somewhat, but removing the dirty +12v completely fixed my voltage issues. I used to have noise with several volts peak to peak, now I have at most .2-.4 variation across an entire datalog.
Second problem I encountered, resets under load. These started after I took care of the voltage issues, whenever I was at full throttle(at ~80% it would be fine) the ecu would reset shortly after boost came on. After a bunch of messing around with grounds and other such things I had helped it, but not cured it. Not wanting to drop $100 on sparkplug wires that might fix my problem, I started searching on msextra.com forums and found that the RSTINV(pin 6) resets the cpu when it drops below 2v. The internal pull up resistor is in the mega-ohm range making it very susceptible to RF noise, this pin is so sensitive that if you touch it with your finger while the engine is running it will reset. It was suggested to solder a .1uF cap across pin 6 and pin 2(ground), the cap will charge up to 5v and hold pin 6 there much more reliably than the internal pull up alone.
I'm hesitant to say that it has completely solved my reset issue, but it's been 2 days and ~100 miles since without a reset.
Anybody else have some good ones they want to share?