Welcome to the forums!
The I'm having difficulty answering your question because I'm really not sure what is the most performance to cost item to upgrade. I've only heard the fully modded ZR2.
The beeswax type I and type II signal caps are higher grade caps than standard.
The bypass mod is also called the 25th anniversary mod. After Steve developed the UFO25th amp he took what he learned from that and offered it as a mod for this other amps.
You read what Lon said about the tube regulation.
If you can swing it I would say get all four. I'll present it in stages.
Stage one: poly bypass mod.
Stage two: Beeswax type II and Poly bypass.
Stage two point five: Beeswax type II, poly bypass and tube regulation.
Stage three: Beeswax type II, Beeswax bypass mod and tube regulation.
please do not hold be to this order of which to get. Someone else might have more experience with the individual upgrades.
Here is a link to Steves documentation of developing the 25th anniversary amp.
https://www.decware.com/cgi-bin/yabb22/YaBB.pl?num=1510887200