The engine probably failed because of the exhaust. Wrapped = excess retained heat. Loud Emgo muffler = exhaust flow incompatible with EFI programming = overly lean condition. Together this means you probably melted or broke the exhaust valve and/or guide and/or the top of the piston.
I understand that riders want to personalize/customize/ improve their ride.
When I carried Enfields (vincesmotorcyclestore.com) I had many customers "fix" their bikes to the point of un-rideability. Can a motorcycle be improved over factory set-up? Certainly, but not by applying the thinking your grandfather applied to his 1935 Model A.
Now you are talking about getting another bike to modify to the point of being a Franken Bike.
My suggestion is to properly and PROFESSIONALLY repair what you have. Reinstall the stock exhaust. Then ride it and enjoy it for what it is.
I have RE customers with over 40K miles on the engines, and other customers with phenomenal mileage on their Japanese bikes. The mechanical commonalities are either a stock exhaust, or a well thought out modification of the entire intake, exhaust, and electronic support systems including EFI remapping. Not EFI modifying.
As for the chain. You cleaned it. Did you ever lube it with a motorcycle specific chain lube? The lube must go between the inner and outer link plates, then allowed to sit for an hour to set up. Even an o-ring chain NEEDS to be lubed every 300 to 400 miles, and every time you ride in the rain. Most people adjust the chains too tight, causing rapid and excessive wear on the chain and sprockets. On any bike you should adjust it to have 3/4 in. to 1 in. play, midway between the sprockets, on the bottom run, WITH YOU SITTING ON THE BIKE. Your weight changes the swing arm angle and tightens the chain.
In 45 years in this industry I've found that most rider dis-satisfaction stems from customer 'improvements".
"If it ain't broke, don't fix it.