Brake chatter and inner tubes

On my first condition inspection I remade the brake lines because my paint shop bent the **** out of them and several people had walked into the "big loops" over the past year. They still worked fine, but I didn't want them to fail at the wrong time due to repetitive stressing. Anyway...

After replacing the lines my brakes chattered like crazy, sometimes even at low speeds and always at higher speeds. I carefully made sure that there was no side-load on the caliper due to the lines, but I couldn't make them stop vibrating. Strangely enough, they vibrated less when there *was* a side load on the caliper induced by the aluminum line, but this also caused them to drag slightly and was not acceptable to me. Finally out of frustration I replaced the last 6" of the aluminum tube with flexible line, beveled the leading edges of the pads, and lubed the caliper pins with graphite stuff. Now it's considerably better, but it's not as good as it was prior to me screwing around with it -- which was nonexistent.

So here are my thoughts. I'd be interested in hearing yours...

1. I did not replace the pads because they're only 50% worn. Perhaps having 50% worn pads naturally leads to more brake vibration because when the piston retracts there is more room in there for the caliper to bounce around -- more room for slop. Has anyone seen this?

2. I did rotate the tires because they were wearing more on the outsides due to the way the gear hangs on the RV-8. This involved splitting the wheels, etc., and mounting the tubes with the red dot on the opposite side of the tire from where it was originally. Could my brake chatter be a symptom of a change in wheel balance caused by remounting the tires and tubes?

3. I know you're "supposed to" replace tires and tubes at the same time, but I also know a lot of people don't do that and experience no issues. Has anyone seen an increase in vibration after remounting a tube in the same tire but with the vavle stem coming out the opposite side?

Thanks for any input/advice.