There should be no “noise” coming from a new clutch job.
On a high mileage clutch, since dropping a tranny is one my most disliked jobs, I replace:
Clutch, pressure plate, throw-out bearing, bearing retainer clips, pilot bearing, tranny input shaft seal and housing gasket, and rear main seal. Unless the flywheel has visible cracks or ridges, I just block sand it with 320 & 400 grit emery cloth. The good thing about having it machined and resurfaced is that will correct any possible heat warping. A new flywheel is not that expensive. If I were to give the flywheel to a good machine shop for resurfacing, I’d have them check and balance the flywheel and pressure plate.
I assume you replaced the pilot bearing and throw-out bearing?
Did you very lightly coat the input shaft seal housing with a grease where the throw-out bearing rides? And, where the clutch disc rides on the end of the input shaft splines?
Usually a “noise” from the tranny will be the throw-out bearing squealing, but can be pilot bearing. The noise can be from a worn input shaft bearing.
The noise may not be from the clutch area. Could be U-joints, transmission, t-case, rear differential, motor mounts, front drive shafts, or rear springs.
Here’s simple description of noises…. for a worn cluch, but may give you some insight into the sounds your are hearing.http://www.2jsautomotive.com/blog/distinguishing-noises-worn-clutch-system/