If you can slowly raise the throttle and it powers up fine, but you snap the throttle open and there is poor response, check the throttle position sensor (TPS). It is responsible, along with the MAP, to provide fuel enrichment on throttle increase (Basically an electronic 'accelerator pump' from the carbed days).
Injector ratings are important, ie: x amount of fuel at Y pressure, because it tells you how much fuel will flow. I'm glad you got a re-map when going to the 350 to hopefully keep it from going lean. the formula for figuring out flow at a different pressure is sqrt(new pressure/old pressure)*old flow rate.
So it would be sqrt(29/13)*90lb/hour = 134lb/hour or so, so a 50% increase or so over the rating. But, as long as the ecm mapping is for a 350 with your air flow, compression and injector size and fuel pressure then you're good.
Really, if they are the same injector size you had before, and were successful with, you're fine.
Keep in mind though, that this rating is in no way the maximum that the fuel injector can take. Some high performance guys run over 50psi with no issues. Your 29psi should not cause any injector lockup.
Hope that helps,
Chay