There's timing hits in the new setup, that aren't in the old. The decrease in timing is likely what's taking away from the full gain of the DP Mod. You're running boost levels similar to what I'm used to and I had timing issues due to octane at those levels. That could be the underlying issue. Most at these levels are running 100% Meth (VP-M1) or E85.
I also don't like your WGDC vs FF readings. It looks like you have PID set high, but it's likely due to that you don't have the EGW Harness. I state that since all your bias settings are at 50/stock. If you do have the harness, you should trim PID down and use the bias to adjust your boost. That will trim down your range of deviation and allow FF to to work more effectively.
This may be a lot of information and may be more than you'll understand without reading up on the topic. It's also a very quick look at logs that aren't proper for tuning advice. I'm using the short 3rd gear pull area for review. There are several posts telling people how to properly do pulls for tuning. Yet, most still don't follow them. Those directions on proper tuning pulls aren't for your daily drive. That's what the FF does. The tuning pulls allow us to get the JB4 tuned so that FF has a chance to work properly for you in all other conditions. Tuning pulls should always be 2k-Redline in 3rd or 4th gear. The higher gear is preferred if there's room, but 3rd works.
Hope this helps... there's a lot of posts with similar information on them. One under the N54 is very helpful, just know that PWM is WGDC for us.
JB4 Duty Bias FF Tuning Info - N54Tech.com - International Turbo Racing Discussion