I have a cheap unbranded focus rail off ebay which works ok. Mount stability is particularly important at higher magnifications.
I don't use a hood at all. There's not much working distance anyway so you don't want to waste it. A filter might be appropriate as I've ran into things with the lens before!
At higher magnifications, the light loss is pretty bad so you might consider a continuous lighting system.
I do have the Canon angle finder but not used it with the MP-E65. In most cases live view is easier unless you're working at odd angles.
Canon 1D, 300D IR, 450D full spectrum, 600D, 5D2, 7D, EF 35/2, 50/1.8, 85/1.8, 135/2+SF, 70-300L, 100-400L
EF-S 15-85, TS-E 24, MP-E 65, Zeiss 50/2 macro, Sigma 150 macro, 120-300/2.8 OS, Samyang 8mm fisheye