Yes, it probably best to stick with the oem coil.
What do you mean "insulate" the blue wire? Do you mean to disconnect it and heat shrink the end?

 

Correct - not used in dual fire operation (as in stock coil). Ensure all switches on module are off (down)

Considering there is no VOES, it's possible the installer grounded the purple violet wire from the module, which would normally go there. If it's grounded, it will cause the ignition to be fully advanced at 1500 rpms like mechanical flyweights would do. If it's disconnected, timing will not be fully advanced until 2500.

If it is grounded and switch 1 is on, it will retard the timing 25 degrees and you don't want that.

 

I apologize if that picture is too big. Thats the current setup of the switches. I havent messed with them at all so thats how it came to me. The violet and green wires coming out of the module are both disconnected (cut and capped off) I did clean up the wiring a bit because a few wires from the starter circuit fused together on my ride home after purchasing it. They were bare wires, a small section was touching the cylinder head. After cleaning the wiring, it was running fine for about a month

 

Sorry to leave you hanging - computer problems last evenng.

The green is for an electric tachometer. The violet should go to voes or grounded (or not) as explained in post 22.

Set all switches "off" for now. You can run switch 6 off with a single fire coil, it'll fire the coil as a dual fire when 6 is off.

Really should try a dual fire (stock type) coil if you can borrow a know good one.

 

Its all good brutha. I'll try to nab up a new coil from harley today. Hopefully that'll fix her up

 

I purchased a used but fairly new looking coil on OfferUp. My coil is relocated to the left side of the motor, so I wired it up as Pink on the rear post and White to the front. My bike also has a grey wire connected to the front post with the White. I believe that's for that ignition key switch. Its the spring automotive type, which doesn't even work, in addition it has a push button starter on the starter itself. No wiring exists on my handlebars, no killswitch, run, or accessories.
Anywhoo, the same problem is present. I'm still planning on buying a brand new coil before ruling anything out though.
The only other thing I can think of (before just taking it into a shop) is the wiring. The wires are old and when I cleaned the wiring up I soldered a lot. I've heard this can raise the resistance of the wire, on top of them being old and corroded.

 

Update
I re-timed the bike statically. Its finally running close to normal as it was before. Hesitation, bogging, and backfire is gone. It definitely took a few tries and doing it by myself was a pain in the ***. In the videos I seen, everyone makes it look so easy!! I wish I'd have done this first though.

Anyway, I appreciate all the guidance and knowledge thrown my way. I definitely learned at least 1 thing... I think. Haha.
Cheers Bromos