First off, look at all the positives. New engine, tranny rebuilt, and a ton of new parts. All these things add up VERY quickly, so you are way ahead financially. I spent way over $4300 and still don't have what you have at that price point. So take a breath....you're good! My wife and I joke, it's my $10,000 ($3500) Blazer. I'll never get what I put into it back. Not for a LONG time!
The slow windows are to be expected. The motors get weak and the as you noted, the window seals need to be replaced. That's one to add to the list.
AC, well it would be a crap shoot if you had it working. A lot of times, they just don't work due to cracks in lines, etc. Do you have rear AC too? To do it right, you'll want to replace all the lines, new compressor, new dryer, new condenser, and then fill with R133, or whatever it is. The R12 is old and very hard to find. And when you do, it's expensive. Just convert it over.
Heater core. That's a job, but can be done. You just have to take the front dash apart.
And dashes....well they've gone up HUGE for OEM. I'd recommend Dashes Direct. Looks to be a decent reproduction.
What tranny do you have? A rebuilt TH400 (3 Speed), or did they somehow put in the 4L80e (4 Speed)? That would be a HUGE bonus!
Paint is a given and expected. Just the norm of these truck. Most important is rust. Hopefully it's minimal. I keep chasing my rust....hate it.