First of all, congrats on scoring a 1st Gen! I have an '88 myself, just finished restoring it. I've had mine for 14 years, and I work for Auburn Toyota as a parts back-counterman. Been there for 18 years, so here's my two cents...
1 & 2) Stick with the 22RE. For the uses you described, the 22RE will be more than adequate, and a 3.4 swap can be VERY expensive. The 22RE, when properly maintained, is near bullet-proof. Just be sure to use metal timing chain guides when you rebuild. I'd also hope you know to avoid the 3VZE 3.0 V6 at all costs, lol...
3) The rear windows are replaceable. Mine was stolen back in 2010, and they broke one of those windows. I bought the entire left side window assembly from a wrecking yard for $50.
4) 90% of parts for these are discontinued, so wrecking yards and EBay are good sources. There's an Ebay seller called The 4Runner House who has different stuff in & out. You can try
Yota Yard - Toyota and Lexus Salvage Yard as well.
Hope this helps...