olthumpa,
Just went back through and re-read this entire thread. I deleted my previous message because, after re-reading, it became clear the throwout bearing was not the issue and shimming wouldn't help matters. I kept coming back to your comment about the arms sucking too far down into the clutch and the travel being limited.
An idea just occurred to me that I think might lead to final resolution:
I'd contact Kubota and get the flywheel specs for the other models that this clutch pack is supposed to fit and compare them. I'm wondering if we will find that flywheel specs changed and your now "properly" machined flywheel is actually machined to the specs for the dual clutch assembly that fit the early 120000 housing.
By taking a look at the other model flywheel specs, we should be able to figure out if the flywheel machining is correct. I'm betting you will find the flywheel machining specs are different. I'd concentrate on getting specs for the newer model tractors because I'm guessing the number of drivetrain revisions had stabilized a bit more.
Per the Madison Tractor site the assembly fits the following makes and models:
Kubota COMPACT TRACTOR: B9200
Kubota COMPACT TRACTOR: L2250
Kubota COMPACT TRACTOR: L235
Kubota COMPACT TRACTOR: L2550
Kubota COMPACT TRACTOR: L2650
Kubota COMPACT TRACTOR: L275
Finally, while searching the clutch pack part number, I stumbled on this site and noticed the pic of the clutch pack looked different. Figured it was likely from a different manufacturer OR, they just used a generic pic dual clutch pack pic. One could always verify that the unit they plan to ship is identical to the pic when ordering... Figured you might be interested:
http://www.reliableaftermarketparts...490/32425-dsh-14200-Kubota-Dual-Clutch/Detail
I'd still go after the flywheel specs first though.
Good luck,
Steve