Lets not confuse things here. Your original question is what can be done to the motor. Most of the items have been covered. I know the FSM doesn't have a limit to what you can deck the head to, so .010 is the allowed amount. (FSM says to replace the head if its warped out of spec) OEM thickness head gasket only. Gasket match 1" into the head (not necessary on the exhaust side, probably not necessary on the intake if you use the OEM intake). I'm waiting for clarification on the cam gears on VTEC engines, but for now I'd say they aren't legal. That is it for the head. The block, you can blue print and balance (but not lighten) and neither of those are really necessary on a Honda IMO. Other then that, .047 overbore max, compression ratio and quench area of the piston cannot be changed from stock. ECU and intake manifold/tb/injectors are open. Underdrive pulleys, flywheel/clutch, header, catalytic and very little else.
Answering your ECU tuning question, yes, ECU tuning is worthwhile and beneficial on these cars. Especially if you can afford to run GT260 and crank the ignition timing way up.
Nate Whipple
NER
188/88 DSP ITR