Initially I considered using the GL1200 EFI setup, and IMHO, if you want to EFI your bike with ITB's, I would say go that route. Going price for a complete setup seems to run 150-200 bucks, and with minor mods will fit a 1000 or 1100. Most of the work was already done by honda, so relatively it's plug and play.
I decided on the 600 throttle bodies because I am aiming for more performance. These are from a 2001-03 model bike, so each body can be separated, unlike the newer bikes which come in joined pairs. This allows me to try and mount them however I want to. They are a 36mm throttle body, which is relatively big, but I don't believe will be too large to hurt overall performance. I won't know for sure until I run them obviously, but seeing as guys are running carbs with 35mm venturies on IDF's and getting impressive performance gains, I feel these should work out fine.
Here are my throttles. They came complete with everything. The wires to the TPS are damaged, but the injectors are all in excellent shape, and overall very nice condition. This is how they arrived straight out of the box. The only real issue is the wires to the TPS are exposed right at the base of the sensor, but I already priced a second one new for cheap. Between a new TPS and these bodies, my investment so far has been $62.

I also scoured until I found some intake runners from a recycler for $14 for the set. I didn't necessarily have to do this, but I figured it would make things easier if riding season arrives and I'm still not ready for the conversion. This had an added side bonus of letting me test mount one of the throttle bodies to the factory boot on the runner... The results:


They fit perfectly. The groove on the boot actually sits inside the notch on the body perfectly, and it's very snug, so there is no chance of them coming out if they were clamped down. About the only potential issue I see is the fuel rail possibly hitting the frame, but I won't know that for sure until I can actually mount a pair up. The nice
Then that leaves me with one of two ideas. I am kind of torn between the two.
First Idea: Making a simple flange with a tube protruding out to allow a silicon coupler to clamp the throttles to the stock plenum, utilizing the stock air filter.
Second Idea. Clamp on 4 shielded air filters straight to the bodies and/or run a set of trumpets. These bodies are about 2 inches shorter than the carbs to the plenum, so there is plenty of room for stacks/filters. For vacuum signal and idle control I can utilize the 4 air ports on the bottom of the bodies and use or make some sort of vacuum block. In terms of work, this would be simpler... and probably sound pretty epic. Plus, it would give me space to mount the ECU where the OEM air box used to sit.
In either case I still have to figure out the linkage, which each presenting it's own challenge, so that's kind of a wash.