Is the goal to have fun and restore this original engine and get it back in the car as original as possible?
Or is the goal to get the car on the road again and make some happy-funtime boosty noises?
It seems like this engine has had a bit of a rough life and if it isn't important that it is THIS engine that powers the car, you might end up saving more money (and work) in the long term if you consider grabbing a gen4 or 5 motor and swapping it in.
Assuming you are dedicated to using this motor, if it was my car, I'd be doing forged pistons ARP studs and a MLS gasket with ACL main and rod bearings so you know the bottom end is solid and you'll never have to touch it again. You're here anyways so you might as well use better parts. Fluids are expensive these days and you're in for a few hundred dollars minimum each time you drop the engine. Especially if you're using the factory toyota MTF gear oil at 50 bucks a qt...
The gen 2/3 platform is really fun with 15 PSI on the factory turbo with an intercooler upgrade and exhaust. That IMO is the sweet spot for this platform, it's really not a substantial financial investment all things considered and it's still a fun ride... it'll be somewhere around 250 wheel horsepower. If you grab a ct20b, you can push a little bit more out of it.
Again, not my car not my lunch money, but with how detuned these are from the factory, I would go with the higher CR and not sweat the difference between 8.8 and 9:1. If decking it up true does end up take a substantial amount of material that would push the CR higher, just compensate that with a thicker head gasket.