Ok man, first decide what you want. Are you going for “more power” or do you want an “All Motor Beast?”
THE HEAD
If you decide to get an ITR intake manifold, you’re going to need a 94+ fuel rail. Aftermarket rails are nice, but you’re still gonna need an aftermarket 94+ model. The ITR manifold will bolt right up to your GS_R head because they both come from a PR3 head. You may want to talk to RedStarGSR about vaccume lines and hose. You’re going to need an aftermarket Throttle body or an ITR throttle body. There are other options, but I don’t want to stear you wrong and I’ll just tell you what I know will work for sure.
ITR IM $225
ITR TB $???
A port and polish is never a bad idea. The “Port” means that they will make the opening on the head the same size as the opening on the intake manifold. This causes less turbulance with the air flow and you’ll have better air speed going into your combustion chamber. This also means you’d better get your intake manifold before you get your P/P job. With porting they’ll also make the openings in the head bigger. The “Polish” means that they’ll smooth out the air ways letting the air easier still.
P/P $???
OEM VTEC cams are never a bad idea. You’ll get OEM reliability and you won’t have to spend an arm and a leg to get them. This is really where you need to decide what you’re going for. If you want a beast, OEM will limit you to 8,600 rpms redline. They don’t make power past this. This is fine if you just want your car to make the “more power” instead of being a beast. I’d recomend OEM ITR valve springs and you should be ok with that. Aftermarket cams will require aftermarket valve springs if you’re taking your engine above 8,600 rpms like me. 
Cams $ depends on where you buy them.
There are other things you can do to the head, but I don’t think you’re after that kinda performance, so I’ll just leave it at that.
THE BLOCK
You’ll want to hone and bore the block. Boring out the block will not only make bores (cylinder walls) smother but it will allow you to use over bore pistons. These pistons are .025mm overbore and you’ll gain a whoping 24.98 cc’s from it.
To raise your compression ratio you’ll need to swap out your pistons. I reccomend the JDM ITR pistons. With these in your block, you’ll have a 10.8:1 compression ratio. You will have to have your rods milled 1mm on each side to have them fit into the piston. This will increase you’re power buy a lot. OEM Honda rings seem to be the recomended rings too.
JDM ITR pistons $250-300
I reccomend that you strengthen your rods and balance your crank while they’re out. Its been around 10 years of driving, why not treat them right. You could get yours shot peened or send them to florida at OneCryo and have them deep frozen (-300 degrees). I also recomending having your rods balanced and your crank too. Balancing the rods means they will shave material off the rods until they all weigh very close to the same weight. Same concept with the crank. If you get this done you’ll be able to live in the high revs with comfort.
Along with all of this stuff I reccomend ARP hardware to hold it all together. Head studs, rod bolts…the whole deal.
There are many other things that you could do, not one alone is going to really make a difference. You’d kinda have to do all of them to see any kind of gain. I’ve talked to you before and I think will this stuff done, you’ll get the results you’re looking for.
-Steve