Too little info....year, miles, mods, tires (new/used miles) ? Oh wait, 2005...mmm-hmm.
Okay, you had new HH pads and installed them when you replaced the brake lines. Nothing touched that would cause a shake there. Are you positive you got all the air out of the calipers ????....even with one side operating fine it shouldn't shimmy. Next question, was the front wheel ever removed, and maybe not reinstalled properly ?. Torquing the front axle is definitely a procedure. Next question, is all the valving equal on the forks, compression, dampening, coil loads ?. Next question, do yo do a lot of wheelies ?. Next question, did you cross-torque the rotors properly ?.
See, you're description is that you broke the pads in after you installed the pads, and the brake lines. This is when the shimmy started, correct ?. Some tech told you that you may have warped a rotor because they're too thin, correct ?. So you put Altha's on, and didn't replace the pads again at that point, correct ?. The shimmy still remained at that point, correct ?.
I'd start by bleeding the front brakes over, per manual, and double check the reassembly of the calipers, then see if the condition still exists. I would also check front tire pressure. If yes, then I would pull the front wheel and check the bearings, and make sure that the front tire is in good, condition. Reinstall wheel, per manual, then move on to forks. I would check all the fork settings and make sure that neither fork seal is leaking also. You could possibly have air in your fork stabilizer also. If the nut fell out, you have might have no stabilization at all. Something's up. More info........
Something happened "after" the first install, but just changing pads and brake lines isn't enough to develop a shake unless something was damaged just prior to the first installation. Then it's just being magnified. More info....
