I also have the Y-link setup, and have had similar issues with the "clunkiness" of the setup. I thought I'd share several things that I had to do to quiet it down.
First off, the ends of the arms where they intersect the belly pan pockets were contacting the pockets in the belly pan. I saw shiny spots where they had been making contact, so I got the die grinder out with a carbide burr and made some reliefs where the shiny spots were.
The other thing I noticed right off was that the boxes in the belly pan (where the arms connect) have been intentionally constructed to allow a "slip" fit for the superflex joints (presumably so it can be assembled by hand). The bolts provided are course thread bolts and like someone already mentioned, -getting them tight is a real chore due to clearance issues. I could not tighten the course thread bolts tight enough to pinch the spools of the superflex joints, and they would clunk pretty bad. When I removed the bolts for inspection, I could clearly see some fretting on the shanks of the bolts, -obviously the spools of the superflex joints were not being clamped in tight enough with the course thread bolts.
SO, I got me some fine thread grade-8 bolts, smeared a bunch of never-seize on the threads (still using locking nuts of course), and tightened the crap out of them. Problem solved (for the most part).
In the instructions, they say not to overtighten the axle-side bolts due to possible bushing damage. I ran the bolts "snug" -but not overly tight for a while, and found them to be a definite source of noise, -particularly when backing up and hitting the brakes. I figured that since the dang bushings have steel sleeves in them anyway, -why not just tighten them down. So, after doing that, -even more noises gone, -and so far, no penalty, even after beating on it hard (will have to wait and see what happens long term).
I have come to the conclusion that the Treks setup is not Cadillac-quiet, but I have been able to eliminate many of the thunks and clunks it had when first installed. I will also say that I beat it HARD out on the trails, -and still expect it to be quiet on the road, -and that's asking a lot.
On the flip side, the Y-link setup flexes like mad, and the on-road manners are better than it was before it got lifted.
The fine-thread bolt idea seemed to do the most good.
My .02
