Cheers Dave, got it all sorted in the end.
I fitted new o-ring gaskets to the valve cover, and the breather cover.
I fitted new o-rings to the dowels on the end caps. I had previously fitted CB500 rocker arms and shafts to the cover, and when I fitted them, I noticed the two 550 ones, were actually a little longer than the single piece 500 shafts, so I put the old dowel o-rings in between the end caps and the shafts.
Also fitted new o-ring to the tappet covers. If anyone else is like me, and was wondering why there was 12 of these in the Vesrah gasket kit, the other 4 fit on the intake runners.
Now I just gotta get out two seized carb sync screws on the intake runners. Tried an impact driver, heating and soaking, but no luck yet. It's a bit hard to get a decent hold on them, and making sure they don't get mangled of out shape in the vise.
Might have to cut the heads off and drill them out.