I've seen lots of posts regarding the engine internals and such, so I won't address that. I'm also not a GTE owner (NA is my thing), so I won't get into specifics of turbos other than to say that while the engine is out, it's an excellent time to get the CT-26 looked at/rebuilt/upgraded.
I tried to write the rest of this post in a conventional format, but I kept losing my train of thought, so I'll present it differently.
Here are some other things to consider doing while the engine is apart, since you don't want to take the engine apart again later to upgrade things that you could just upgrade now.
- Replace/Upgrade your valve springs. A70 Supras are not new cars by any means, and valve springs do wear. If it's in your budget, you may want to consider an upgrade to something with better performance, or at least new versions of what you've already got.
- Replace Valve Stem Seals - These are notorious for going bad on A70s, so a new set while the head is off is just common sense. You should probably be slapped if you put the head back on without replacing these. New valve stem seals should be made of Viton or Viton II.
- Oversized Valves - While not critical for anything near your power goals, oversized valves will further increase the ability of your intake system to push air into the cylinder. As we all know, increased air is required for increased power, and a better-flowing head will get more out of your turbo.
- NA Cams - There was a lot of controversy about this for a while, but as long as you're aiming for under 500HP, NA cams are cheap and a perfectly good alternative to new cams. The timing of valve events (most notably the opening/closing of the exhaust valve IIRC) is slightly different on the NA. This leads to increases in power for turbos that aren't shooting for the sky. You'll have to replace a couple other parts while you're at it, but the upgrade is definitely worth considering.
- Lightweight/Adjustable Cam Gears - Less rotating mass, even if only slightly less, is still less work for the engine to do. Adjustability is also a good thing to have since you can tune the cams for even better power/torque.
- Electric Fan - Replacing the belt-driven fan for an electric fan will lessen rotational mass and provide an appreciable increase in ability to rev. Who doesn't like that? It should also provide 2-5 previously lost HP. This could come in handy when you consider parasitic loss in the rest of the driveline. On top of that, electric fans provide consistent levels of cooling in all RPM situations and make general access to the front of the engine easier.
- 3000 Pipe Upgrade - The stock 3000 pipe has been shown to be somewhat restrictive. It's a shame to get all that air flowing really well and then choke it off even a little at the 3000 pipe. There are larger ones out there, you might even be able to find an HKS version.
Also, you can replace the driveshaft with a 1-piece unit and reduce some parasitic loss, but that's completely separate from removing the engine and has little to do with the thread. At any rate, since the motor and tranny will be out there's little reason not to do it. You're already taking it halfway off to remove the transmission, right?
That's everything I can think of outside the block/internals. Take or leave what you wish, it's probably more than you can afford to do all of it. Some things like the piping/exhaust upgrade can be left until later, since they don't require disassembly of the engine to perform. Also, these upgrades are fairly small in nature and at the very bottom of the mechanical pyramid. As far as I can tell, there shouldn't be any supporting mods required in order to use the things I have suggested, apart from upgrading the CT-26 which may or may not require an AFM/injector upgrade depending on how far you go with it.
You have to buy new rods unless you absolutely want them or need them. Shot-peened stock rods have been shown to handle 500HP before having problems.
Be aware also that with a FFIM, there is definite potential for uneven air distribution in the cylinders. Make sure it's made well, or you might find some cylinders running lean while others run rich.
A final note: This may be painfully and ridiculously obvious, but increased horsepower requires an equal (or greater) increase in brake power. 0-60 is much less important than 60-0.