Is the fuel pump stock?

 

you can boost a reasonable amount on the stock pump even. if its fine during cold start and gets worse as it warms up its a lean condition causeing your breakup, which makes complete sense you have changed the VE of the engine, and it likes that extra cold start fuel you are feeding it. you need larger injectors or a fuel controller.
I would advise larger injectors, cause if you use just a simple piggyback to increase the map signal in the case of adding fuel with stock injectors, you are actually lowering the psi you will hit boost cut cause the ecu thinks the load is higher than it really is, and as a sideaffect your timing map gets more conservative means you loose out on some power. get some 440cc injectors and it will run better and retain the stock timing map. get some 550's and a fuel controller and you will be probably trimming out some fuel instead which will raise the psi you hit boost cut at over stock, give you a little more aggresive timing, and add some adjustability. or you can go standalone and not need to change anything and run whatever tune you want.