Hi Randy, I cannot answer all, but I like your application. I am a former road racer. Last bike was a “sounds of Singles” Honda NSR framed XR600. It too ran one carb for each intake port/valve. My recommendation is to think the same with FI. Not sure what you had in mind. If you are thinking to make it a Siamese port with one injector and throttle, it might be a tad easier and less expensive, but you will be robbing some potential.
I would keep with two independent throttles. You will only need one controller for both and coming up with tuning parameters will be much easier, as you can get the fuel flows from Mikuni or Keihin. With FI your throttle bodies will be bigger than the carbs. There are many thing to consider…like compression ratios. Yours is likely 8.5:1 range versus the newer bikes around 12:1. If I were guessing, without data, I would think that you would have two 38 mm bodies or if you choose a single, possibly a 42 to 44mm.
For comparison, the newer Kawasaki KX450F models have a single throttle body that is 43mm. Yes it is only a 450, but it is rear 13:1 compression and liquid cooled. Might be a place to start, as the head flows could be in a similar realm, total flow-wise.
FI bodies do not have the same air flow characteristics as carbs. There is usually a bigger difference in diameter inlet to outlet, thus higher velocity than a carb. (More air volume) Beside the KX, look at the TT650RE from the early 90’s. Same compression ratio as yours, but a different carb setup. A funky two stage that the Yamaha engineers loved. If you can find volumetric flows for that setup, it might help.
I have been doing much work with Honda CBR and CRF 250/300 engines. The 300’s run a 38mm throttle, the 250’s a 36. One setup for a 250 is to upgrade to 38, plus cams…You can buy those cheap from an OEM supplier or find them on eBay for sale. Then use the Nano EFI when available. Wide band O2 sensor should go in the collector.
I am sure Travis will have a “wizard”. Even the wizard, uses his own wizard…or magic wand.