So the R&P set is going to make my NSX accelerate faster off the line but reduce the top speed?
Yes.
and with the short gears, that just makes it so that when u shift, it puts you in the best place in the next gear rather than changing ratios right?
The short gears put you in a better place when accelerating and upshifting from first to second. They do this at the expense of putting you at a worse place for the upshifts at higher gears.
are there any other down sides to the short gears or R&P other than the obvious?
Well, there's the obvious one, the cost of the upgrades. Also, they may not give you as much value as spending the same money on upgrades that will give you more power. This is written up in the "What are the Numbers?" part of the "Gears" section of the FAQ. Compare the acceleration of gearing changes with those of adding 20 hp, for example.
Also, look through this same section for other downsides, like increased noise with the 4.55 R&P, as well as the previously-mentioned fuel economy decrease.