Alright fellas.
I got the original box working again! Went through and reflowed the board, found a couple that bubbled out when hit again. Fixed the cap leg and used some gorilla glue epoxy to cement the black capictors. So I rode it the 3 miles to work today with the plugs gapped at .015....
-Roll in is smooth, still hesitates when you give her the whip.
-5th gear miss is still there but not as prominent as before, closing the gap helped that out a lot!
-She started to break up about a 1/4 mile from work in 3rd, going up a hill.
We're probably all on the same page here. With the gap closure advice from TwoManyXS1B's, and a return to a baseline with the original black box. I feel pretty confident that the coil is seeing an intermittent failure, due to a bad winding or heat soak. I'll get coils situated and hopefully that will clean it up. If it does then I'll swap the replacement box in and see if it clears that one up as well.
P.S.
Side note: I just ran to the store and it died on me again, no lights. I had to cycle the key to get my lights back, and she fired right up. I have an O'Reillys car ignition on this thing and I'm starting to think it might just be vibrating it's self off? I have it wired power out from Bat to 20 amp fuse, then Y to rectifier and ignition. There's nothin else on the battery side of the ignition and everything is soldered in and shrink wrapped. She ain't blowin fuses so the dieing issue might be the key? Don't know what else would kill the whole bike like that.