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There are boondocker controllers for both the 800 and 900 EFI. Also, aren't there some that just go right on the injectors? Those should be pretty universal.
We are doing the 975 big bore with a single in the Dragon (carbed). One of my buddies is doing a stock 900 EFI, and he actually had more trouble with clearance than we did. Throttle bodies are wider than the carbs.
The only issues I have with the 1150s and bigger are finding parts for them. That's mostly why we've stuck with the 975s. No current stock motor (non-turbo) feels even close, and parts are easy to come by.
You might be able to use some angled carb boots, to help with clearance.