I had mine apart yesterday so I kind of know about the parts you mentioned. I'd wanted to get some grease on the bearings under the clutch but I gave up because the little puller did not seem to want to remove the clutch. I was so afraid of screwing things up so I gave up. I don't really understand why your pads would not be all at the same height but why could you not sand or file them down a bit. Seems like you don't have anything to lose and it has to be about the simplest set up I've ever seen. Do those pucks just sit in place?