Seeing the fastest box route would be interesting, but switching from 'aims for fastest time' to 'aims for fastest in game time' halfway through a run probably wouldn't do down well here. It'd probably be fastest to go through the game to get the running shoes and then back through with them. I'd watch a 100% run, but it'd never be accepted here as it would be very repetitive.
Like I said above
Joy2Key is a good way to go if you want to use your controller, but if keyboard suits you then that's cool.
Also, you may want to record a (very half-assed) test run first to make sure that (1) the game is emulated properly/at all all the way through; and (2) you should plan a 'mask route'. Using the mask saves 1 second per use in Crash 2 so it should be the same here. If the three masks take you more than one second out of the optimal route then it is not worth it. Also, certain levels take your collected masks away automatically (it is the 'boulders' levels in Crash 2 so it may be more frequent here as there are more different types). Because of this I wasn't able to find much use for the invincibility, but it is still worth testing. Most importantly however, is that just having a mask and taking the damage can get you by certain enemies and timed objects faster (I do this in one of Crash 2's sewer levels quite often, but I can't remember which one), it may also open up different routes. A test run should only take a couple of days, alternatively you could just watch SDA's speedrun to see where the masks are placed, but I don't think that that method would be as reliable.