petrock
At the risk of making this sound like a lecture in the fundamentals of mechanics/performance (it is) let me say this about that.
Cooler air is denser air (always). Anything one can do to cool/reduce temps of the air entering the engine, in theory at least and almost always in practice will further improve performance. When you get rid of the plastic back plate that has some insulating qualities and replace it with an aluminum one, one that is a very efficient conductor of heat you are going the wrong way in that regard. Spacing the back plate away from the heads and upper jugs will allow more air flow between the back plate and heads and the heads will also shed heat more readily. Now, if one was to make the throttle body to back plate spacer and breather spacers out of a phenolic (high insulating qualities) material you could further reduce heat transfer into the plate which in turn reduces heat transfer into the air stream. Here in Souther AZ for example where you can find yourself out riding in 115 degree temps every little bit helps.
As far as the spacer itself hurting performance, (chuckle) the spacer does nothing more than increase plenum storage and tune for a slightly lower rpm, one offsetting other for the most part with such a small (about an inch) increase. Doubt very much you could find it (improvements) on a dyno.
I don't know how tall you are, but at 5' 7" with my skinny ass parked in a stock Bob solo seat I have plenty of room to tuck my leg in behind the air cleaner against the tank. Once I get a round cover on and that safety bump carved out of the seat back so I can slide into a more comfortable position I will have even more leg room.
