I've been pondering it the last few days. I believe I've come up with my answer.
I'm going to pick #1.
The reasons are this:
At #1, I'm at the bottom with only 1 direction to go. Up... (Provided things work out). This also allows me to work on my resume so if things don't work out well here, I can find another job and I've added something to my resume.
At #2, I'm going in there and they are thinking I will help them conquer the world. What if their vendor software can't be modified as easily as they hope it can, and I can't fix the world for them? They are going to be disappointed. I have more potential downside here than I like. While it has some nice solid pros, it is not a software shop, and I'm going to be the only resource here. It's higher risk.
I'd rather get 2 years of experience at place #1 (it's also an established company) which would then allow me to get a job pretty much anywhere going forward. If I pick #2, I'm good while I'm working there. If they get disappointed in what I'm able to do, and I'm out of a job 2 years down the road then I haven't gained anything. I did a lot to really be in the same place as I am now. And I don't want to have to be put into that spot and have to worry about that every day I'm at work. That's what happened at my current job (and why I went looking to begin with -- I was the only resource that was able to do what I did -- and having to make everybody happy) and I don't want to place myself into the exact same situation. All things considered.
Thanks all for your opinions!