I have a 69S -- got it last October. I assume yours is a new one -- the trem assembly was redesigned about a year and a half ago. I noticed the mechanical noise also, but it was just that the arm, when screwed in still has some movement --  some wobble in the holder. I used one of the hex wrenches included with the guitar to tighten the screw on the base of the the holder -- didn't tighten it way down, just enough to take the play out of it. It took the wobble away, and the arm no longer causes the noise. The piezo pickups for the Variax models are on the bridge, so also pick up any mechanical noise that happens at the bridge. I do not use the tremolo arm in my playing (I remove the arm) so I do not have a feel for what others experience. In the few times I've messed with it, it did not cause any noise problems once I adjusted the set screw.

On the low e sounding dull -- it depends on the variax electronic model you're using -- some are brighter than others on the bass strings. It can also be the strings need changing. That's usually the first thing I do whenever I get a new guitar, as you never know how long they've been on there, and I have my favorite strings I use on all my electrics. In the case of the 69S, I actually left the strings on it for a while and used them out live for about a month as they were in good shape, so I just left them. This is my 2nd JTV, my first is a 59, and I remember changing those strings right away... Usually when you change guages or even brands of strings in the same guage, you'll need to tweek the intonation a bit. Also will need to if you change your height set up, etc.

One other note -- if you change your strings on the 69, I recommend you don't take them all off at once. The internal trem springs will pull the bridge away from the 2 posts on the top of the guitar and snap it back against the body (with a POP). I didn't like that. I read about it on these forums, and also experienced it a few times when I changed the pickups and couldn't avoid taking the strings all off. It was a booger to get back on right -- felt like I needed a 3rd hand. I found that I needed the trem arm to hold the bridge down until I had 2 strings in and the tension on them before they would hold the bridge in place. One way would be to remove & replace one string at a time, or if you want to oil the fretboard, leave the 2 outside strings (high e & low e) on, then replace those 2 last.

Anyway that's my experience with it.... YMMV

Dave