I do remember some graphics problems, but, they were just general problems... Speed was OK on my Pentium 3 900 mhz, nice, steady 60 fps.
As for GoodWindows and GoodN64, just set it to rename the roms (you'll see it and hit your head againts the wall if you find out how to use it [it's so easy

]) If it winds up with a [!] after the rename then the rom is a "good dump" If it's not, then, you'll have to download another rom and hope it's good. One thing you don't want to do (just reminding you if you know) is ask anyone here or contact them in any way asking them for roms, that's completely againts the rules.
Other than that, keep posting and I'll check out the game on my end. (yes, I have it)
*My Personal Opinion on MegaMan 64*
The game is crap on the N64, really. If you're going to play Mega Man Legends, might as well do it on the original console (PSX)