Depends on how in-depth you wanna rebuild it. You could go all out and get the cylinders bored or just honed, which you can hone at home. I'd measure the bores to check for roundness, though. If you happen to get a low-mileage one and the cross-hatching is still strong and even, then machining wouldn't be necessary. You'll need a special tool for the cam bearings. If it were me, I'd spend the couple hundred bucks and let the pros with their special tools and equipment do all the cleaning, measuring and bearing replacing. The heads can just be cleaned and checked for flatness and get new valve seals at a bare minimum. But, it's always nice to have a cleaning pass on them to ensure a flat surface. Since they'll be set up on the machine for the cleaning pass, you may even entertain a light shave to boost compression, depending on your goals. Maybe nix the shave and get thinner head gaskets. Maybe have the shop minimize the lump in the intake runners and blend in the bowls for more CFM. This all depends on what you want out of it as a whole. I'm a fan of high compression (10.5+) on an NA engine, but this demands 89 or 91/93 octane fuel.
This is half true. In the earlier years, pre-'04, the LQ9 was the same as the LQ4 except for the flat top pistons. Around '04/'05, the LQ9 got beefier rods and full-floating wrist pins. If you wanted to, since you're rebuilding it, the money you'd save getting a "boring" ubiquitous (and, therefore cheaper) LQ4 could be put towards aftermarket flat top pistons, making it an LQ9.
Built right, you can make an LQ9 an "iron LS2". The 80lb difference is kinda negligible and the overall cost would be less, depending on how wild you get with it.