You must put your MAF sensor back in. The UTEC 3.1 is boost based after 60% (default) tps, but your stock ECU is MAF based.
Your UTEC offsets the ECU fueling so you always need the MAF sensor.
The reason that your #1 and #2 issues resolved is that you forced the ecu into panic mode so it's running rich. Would be my guess anyway. Please put your MAF sensor back in.
Knock is usually down to lean fueling, too much boost or too much timing advance. Sounds like you have a mixture of these.
If you want to run higher boost you will have to check your fueling. You also need to lower your timing numbers.
But to make things easy put your MAF sensor back in and the run some UTEC logs and post those so we can analyze them.
Are you running the Octane challenged map from TurboXS, if so you should be.