Hi ONeill and welcome to the forum. You made a great bike choice, I've had my stock '83 KZ550LTD shaftie for about 2½ years now and really enjoy it. My clutch cable routes, as you said, under the plastic cover & left fuel tank section, alongside #2&3 coil, across the rear valve cover and just in front of the choke lever then towards the clutch. I re-rerouted it slightly when I first got the bike as it was binding against the wiring loom and steering head. You will probably have to reweld the center stand arm or gussets at the point where it bent. I found it is easiest to put the bike up on the centerstand if I first roll the rear wheel up onto a 2x6 board.
Best of luck with your bike:)
