Scoot, Sorry to hear about your situation! What a bummer! I don't know for sure if a later EFI engine will work or not, but I can't think of any big reason it wouldn't. There are probably years/models that would work better than others. I would anticipate that no matter what, there will be a few challenges to overcome as there always are with these kinds of things.
One thing to keep in mind is that the air-cooled Scrambler engines used the 270º crank, where the other Bonneville/Thruxton models used the 360º crank. You will either need to be OK with that subtle difference or make sure the replacement engine is a 270º. The America and Speedmaster also used the 270º engines.
One source for an engine you could contact and/or watch is rubbersideup.com. I have purchased engines from them with no problems.
You could also have the engine rebuilt to a higher performance level by Bonneville Performance (
https://bonnevilleperformance.com/product/high-performance-crate-engines/), by master Triumph mechanic, Bill Gately. Bill would also be the guy to ask about your basic question.
For your reference, I had my 2008 865cc engine rebuilt to an 1100cc engine with the specifications on that web page. It puts out over 100 HP and over 76 ft. lbs. of torque.
You can also read about a 2014 Scrambler project Bill did for a client here:
https://bonnevilleperformance.com/2014-scrambler-project/
I've looked at having the engine rebuilt not had much luck and I don't do main dealers. Does anyone know if a later fuel injection engine will fit my bike if I fit my carbs? 
