Honestly, the documentation wasn't that great is a big first. Lots of misprints. Checking the 4L60E stuff (at the time anyways) was a good way to validate. Second off, the input circuit for the VSS singnal hasn't ever worked. It tends to amplifiy noise more than anything. I've actually talked with a few people who have gotten that working by just eliminating it and using an IC or two.
There's definitely a learning curve getting the CAN stuff going, you have to tweak the configs manually as they don't give you check box options to do it automagically. If you don't tweak the settings it bricks the MS it's attached to and you have to reflash. It's dependent on the code (B&G vs Extra,) and I didn't notice it because it was buried in the site somewhere. Hell I went looking for it so I could get a link and am having trouble finding it again.
Also got banned from the msgpio forum for asking about it a few years ago and the thread I started deleted. Naturally not too keen on that kind of "support." It seems as if their stance at the time was "no one is posting there's problems so there's not any." I have my suspicions of why there were not any posts of that problem. Shout outs to ashford at theturboforums.com for helping out with some stuff including a new VSS circuit and getting the CAN going.
I've got an MS2 V3.0 in the van right now. If it wasn't for the fact I have an early trans I'd probably have gone to some form of the 0411 with Vortec 350 code. That's a pretty damn steep buy in though, and I'd have had to have figured out the crank sensor too as well as rewire yet more than I already have.
I will say, that the integration with MS is awesome. You can do neat stuff like pull timing on shifts which is really handy if you want to run to the ragged edge. It's also really awesome you can tune it from one place. I will expand on that, tuning it isn't actually that bad. The initial table included with it sucks horribly, but I think I threw a screen shot or two in the build thread below to help with that. The idea is of course you hit the jam pedal it's going to down shift as much as plausible. The mid and low throttle stuff probably needs some more tweaking, but it should be pretty close.
Few links, first thread is my build of this beast. Second is a bunch of hints on getting this thing running. Overall I wish I'd have just bucked up for a commercial TCU, my sanity has a price. This will get you a lot farther along for a lot less headaches though.
http://www.theturboforums.com/threads/364550-Megashift-build-for-4L80E?highlight=megashift
http://www.theturboforums.com/threads/371628-Question-for-the-electrical-sorts?highlight=megashift