A few points here. If they used an 11" single mass flywheel kit, you are GOING to have rollover noise, Get over it. If you want it quiet you need to use a 12 or 12 1/4 " setup . The 11" only have 4 springs in the disc hub, half as many as the DMF, the larger ones have about 9, roughly the same as the DMF, so they absorb the torqhe impulses from the engine instead of sending them straight to the tranny input shaft.
If you want to quiet it down a tad, switch your lube to a 30 or 50 wt synthetic ATF, and at the VERY least you should have reguler Synthetic ATF in there, but not plain ol dexron , THe spec for the Zf5 in a diesel was changed a long time ago to at minimum to be SYNTHETIC ATF , a 30 or 50 wt falls withing the original grade specifications for the box. I personally run Amsoil 50 Wt synthetic ATF.
Whatever you do, DO NOT OVERFILL !!!!! the only thing that you will accomplish by doing this is to overpressure your seals and wind up with lubricant on your nice new clutch. If you dig around you will find TSBs on this from basically every tranny manufacurer in the world. They set lube levels to where it has to be dipped up by the lower gear cluster and carried to the upper cluster and runs back down into the bearing shaft. THis is a tried and true design. If you attemppt to dampen the shock impulses in the top shaft by bathing it in oil, you are exposing the seals to lube under extreme pressure that they were not designed fo, they were only designed to deflect spray.
As far as clutch position, any time you throw an aftermarket clutch in, especially with a flywheel change ( especially if spacers were missed ) you can end up needing an adjustable clutch master pushrod. About $11 at Napa will take care of the clutch adjustment problem
