P1545 - tuning or something else?

As the title says, I have a P1545 code that is intermittent. For reference, car is a 2012 Audi A3 quattro with manual transmission swap, genII GTX30, and IE intake manifold. Car currently has APR stage 3 software which is not for the modifications I have currently - the plan is to get it reflashed to stock so I can tune it with HP tuners.

I had the code stored in the ECU, and tracked it down to a faulty throttle body sensor. New throttle body confirmed this, once installed and adapted, the code went away. Now, when I get into boost, the EPC light comes on, and the car goes into limp mode, only letting me go 10-15 mph. If I turn the car off and start again, the EPC light does not come on and the issue goes away, until I get into boost again.

My question is, is this a tuning issue (such as deleting the intake manifold flaps) or do I need to hunt this down before I start tuning? Thanks in advance for any help, I appreciate it.

Nick,

I'm a bit unclear on something you mentioned. You said replacing the throttle body resolved the code, but are having limp mode and a light on now. What codes are present currently?

Thanks.

Same code, but only after getting into boost. When I installed the new throttle body and did the adaptation, the code went away and didn't come back until going into boost, about 5500 RPM.

I'm thinking that this might be an overboost issue, as the car should be producing more boost than what the software is demanding. One thing I forgot to mention is that previously I had a large canister internal wastegate actuator (garrett, 18 PSI) but am now running a tial 21 PSI actuator.