When it started with this condition, I added the fuel pak hoping that was the problem.. it made a significant improvement in smoothness of the engine but had no effect on the cutting out and stumble....
If a normally good running engine develops a problem, never add something to the mix because at best, it will only
cover up the root problem. It won't ever fix the root problem. The bike did run good without the fuel pack, so get it to run good again without it.
You have to correct the root problem first and that means temporarily removing the fuel pack. You really want the problem issue at 'full strength' because it will help you identify it more easily.
I would try leaving the pipes as is, but put the bike back in factory trim as far as FI, ignition and electronics. This way there is nothing between all the external sensors and the ECM. While resolving a problem, I would not want any piggy black boxes included in the mix.
Once you get the (factory trim) bike running like it should,, then stack or add whatever you want to it.
Not that it is related to the engine cutting out, but it's a huge advantage to have the Ion knock retard feature working on the bike. Especially on an air cooled engine where the head & combustion temperatures are all over the place because they are a function of the environment your in. In my opinion it's suicidal not to have the feature working.