@David Baer
Have to agree with @Jonathan Klemm here, it is very possible to get yourself into analysis paralysis. That said, you should be as thorough as possible and try to anticipate every scenario. I will tell you from my own personal experience, both as an investor and GC, there is almost always something unanticipated on every project, no matter how bare bones the start is.
I'll give you an example. We bought a big three family over the summer that was a full gut, there was nothing in the house except for a bunch of garbage. No pipes, no wiring, nothing. Foundation was in great shape, so we assumed we'd take it to the studs and start with our roughs. As we were doing demo, we noticed the rear of the building was swaying...long story short, we had to re-frame the entire back half. And when we removed the existing siding, all of the wood came off with it, so add 100+ sheets of plywood (and labor). All that said, I'd still do the deal again. We bought it well and built in contingency.
You will encounter issues on every project, and if you have one that goes exactly according to plan, consider yourself lucky. But that's what this business is all about and why you NEED to buy right upfront.
Best of luck