I think it would be best to use whichever machine you are most comfortable using and feel you yourself can make the best cuts with. Leaving the hood on will always pose some amount of risk that you could cut something underneath it. As for taking the hood off you can use something to mark where the hinges set on the hood now and that will give you a pretty good guage on where to line it back up on the hinges after you are finished. Should be just a matter of 4 bolts to remove though you may need someone to help you. If you would feel more comfortable leaving it on you could put something underneath while you cut to keep any blade from hitting things you do not want to hit. or you can use something like the dremel which is not going to go deep enough to really cut anything.

Really the biggest thing is what you feel comfortable using and being able to make straight lines with. Also putting tape along the area you plan to cut will help reduce paint damage.

thanks guys. the main thing i have a question about with the hood on is trying to get the vent holes lined up without hitting the supports on the underside.

are there some measurements somewhere that i can use? im a directions/ numbers kinda guy...lol

haha....that would be great if you could adam. im assuming the hood crossmembers/supports are all the same on all the years then