Want to bring this thread up to speed. I've had a long conversation on the 60*v6 forum about running the megasquirt with the odd crank reluctor that comes on the 3500.
Long story short (kinda), the trigger setup on a 3500 is similar to that of the LS2 engines. The Megasquirt supports the LS1 trigger which is a 27x version, however the ls2 and the 3500 triggers are 58x (or 60-2). The LSx setup is a coil on plug (or coil near plug) setup. It has 1 coil per spark plug. The 3500 is the same technology but it doesn't have the coils on or near the plug, but it uses the same setup to fire the coils as spark waste. As far as support for the ls2 trigger, megasquirt basically says that it will work in theory, but it is not confirmed.
There is also a good bit work required inside of the megasquirt to get it to understand the crank and cam position sensors, and to get it to output 3 different spark signals (spark waste) without using a ICM. They did however, leave me a nice "prototype" area to build the rest of the components to fire the three coils and there is a very good write up on how to do it.
The problem for me is, the write-up is designed for a v8. So I would have to plot out the entire reluctor and program the software to understand it. Its just a simple matter of telling the megasquirt how many signals to expect and which ones to skip and which to use.
It'* a lot of work to do, but I could sometime in the future loose the coil "brick" and run a true coil on plug setup... which would be awesome (bragging rights). I would also be the first one to transplant a 3500 AND use the factory reluctor setup (bragging rights), not to mention that I could confirm the compatibility of the LS2 ignition setup with the megasquirt community (bragging rights!).
On the other hand, I could take the easy way out and buy an external crank trigger from wot-tech. It would output the 7x signal that most gm DIS v6 engines use. It would setup me back $160 though. With that I wouldn't have to change anything inside of the megasquirt and use the ICM and coils that came with the TGP.