The RD350 with FI was using a Megasquirt computer to control the injection. I read through his stuff with quite some interest but he doesn't say if it was any good or not. I believe that the same guy now has the motor fitted to a Cagiva Mito.
This guy used the carbs of an R6, fitted the injectors and built the fuel rail. That was probably the easy bit.
If you have a week with nothing to do then read through the Megasquirt manual (it's online) and see how it's done.
Certainly not the case of throwing a couple of bits of pipe on and pouring the fuel in, but maybe not as complicated as evyone thinks....maybe.
Concerning carbs vs FI. The beauty of FI is it's intelligence. Once it's set up, and if you're measuring enough parameters you can pretty well tune it to any situation. My mate's got an Aprilia SXV450 and we've already had a bit of a play and it's quick and simple. Now got the Tuneboy for it, so can really get stuck in.