The combustion stability limit issue, you may be able to enter higher than max value indicated in max map in the combustion stability value (44821). I'm not sure that the HPTuners indicated limit is correct for this, I've seen SCT show higher max values but I don't have it on this PC so I can't say what the theoretical max is.
Indicated torque limit might be table 38136 Inverse Load Clip. You have 2.00 entered in all the cells but are exceeding that in your log.
For throttle errors, I use a chart with ETC Vacuum vs Effective Area and plot ETC Angle Error and enter that into HPT's Effective Area Calculator as described in
this post to cure any TB related error if you know your torque and inverse torque tables are decent.
Some of your speed density max map values may need to be raised as well to see the increased boost from the bigger blower.