would I make anything getting a VAFC tune on a completely stock 03?
stock intake, header, cat and exhaust

I know my 03 seems to have more power stock than my old 00 car.

 

Go for it, i'm sure you can squeeze out a few ponies some members have tuned completely stock; I know of one that was tuned stock on Emange Ultimate and gained 15hp!

 

MY00 and MY03 make the same power. MY03 tho have better part throttle tuning/response. You can lean out with a vafc to get close to 10whp peak... and even more after 8krpm... the S2000 seems to run real rich after 8K.

 

No you will make more power tuning a 2000 and 2001 than a 2003. The '00 and '01 run really rich stock where as the '02 and '03 run leaner stock.
You should still gain a little bit with the tune but not as much as an earlier AP1 will gain.
With an intake and dual exhaust stock cat I gained 10whp peak and 18-20 above 8500 with my vafc1. That is just with tuning not before mods and after with a tune.
You can also lower vtec a little if you want which is nice to smooth out the transition. I have mine set to 5500 and I really like it there.
Also part throttle tuning with a vafc is pretty useless as it will lose the tune quickly as the ecu relearns the stock map. You have to keep resetting the ecu if you want to keep a partial throttle tune.

 

you may make some power I believe the money could be better spent else where on an otherwise stock car

 

Money wise NA a vafc will give you the best gains per $1 spent! That and a test pipe. Everything else just costs a ton for very little gains.

 

Mine cost me about $500 with tune and harness and I gained 14 whp. I had some mods before hand but I went from 204whp with mods below to 218whp with VAFC tune. I'd do it again.

 

alright maybe I spoke too soon... but if he gets Vafc and tune now he will have to pay for a retune everytime he gets a new mod right?

 

Well he won't have to but would def benefit him to do so. I haven't re tuned since I put my test pipe in. Should but don't really want to spend the money on tuning. Maybe gonna cough up the dough and go FI so kinda a wast to spend $200 on a retune if I'm gonna be upgrading soon.
If he get's tuned now completely stock and then puts full bolt ons I think it would be a good idea to get a dyno or at least check the afr's.

 

I might go for a test pipe, header and intake as well

not sure about exhaust I think the stock one is ok just weighs a lot, I don't like loud