Chiming in here.
I also went thru this exact problem.
My first major problem was the flywheel.
Then the balancer cleaned it up a little more.
I was being cheap and didnt wanna replace my 10k miles dual centerforce clutch setup since it was still working great.
But sure as ****....and common sense should have directed me here.
Think about it.....you have a wobbly flywheel vibrating to hell,the clutch disk is taking that abuse as well as the pressure plate.
So..............now one or the other are m ost likely comprimised.
in your cases prlly the resurface was poor.Mine sure was.
You prly have a warped pressure plate......or the disc.
Mine stoped as soon as I changed the clutch.
The trans dont have enough rotating mass to cause a vibration in the motor at nuetral.
Although the input shaft will always spin because its in the flywheel and the flywheel is bolted to the motor.....
IN nuetral basicly only the front parts of the tranny are spinning which is the input shaft and a few small gears.
I also have poly motor mounts and poly trans and poly everything.
You could see the vibration in my steering wheel intensly when the motor vibrated at those certian rpms.
just to ease your worries...
if your crank was bent.........the vibration would get worse as rpms climb...you prly drive thru the vibrations after 3k 4k rpms right?
So..........that reallly leaves nothing more to guess.
You may have had the dowel pins put in a hair cocked or one of the bolts cross threaded ,could be a loose bell bolt even...check the upper bolts on the tranny for tightness and all the bolts for that matter.
If you feel the vibration in your shifter in neutral.Its something I just mentioned according to what you been thru.
Ill give odds that your pressplate/clutch disc are the cause
this is interesting
http://www.vibratesoftware.com/html...gine/first_order_engine.htm#Crankshaft Pulley