I just got the same R1 rectifier from on 05 model, and it's a big clumsy sucker!!! How did you cut the cooling fins down? Is it possible to cut "too much" off of it? I just don't want to mess this up, I have a dremel, and was assuming this would be the easiest way to cut it, I'm going to mount mine under the passenger seat like you did!!!!!!
These units do cool efficiently but you should only cut off what you really need to.
The V-max doesn't rev as high as the R1 so the normal and upper duty cycle on the unit is lower on the V-max. It shouldn't get hot even when the V-max is running in it's higher rev ranges.
I used the paper thin solid abrasive wheels (black disks) supplied with most dremel bit packs. They cut through the fins very easily and quickly.