The tunes should be very similar as long as you are running the same injectors and maf combo. I don't see a reason that it won't work with your goal of 250whp.... For that I think that you have the perfect plan with what you have. Hell, if the s14 t28 is ball bearing and your setup was designed around that, I may use that setup if I were you. Keep the gti-r for later down the rd and sell the s14/avenier setup and get either the screamer dp of an external gated gti-r manifold. Sounds like the s14 turbo would be slightly more reliable and should spool a little quicker. For your current goal that might be the way I would go. I would have to actually see everything in person or at least in pics to know for sure. If everything that you have was setup to run the s14, I would probably run that knowing more about the situation. Sell the other turbos and save for another setup down the rd. The s14 turbo will make more than 250whp so you still have room to grow and it sounds like it is in better condition. More than likely after 2 years you will want more than a gti-r anyway, lol, so sell which ever turbos you don't use and throw that money into your car fund since things can always come up such as clutches and transmissions breaking. That way you have a fun car and reserve cash for disasters since no matter what you do something will always come up.
Drew