You may need to start by balancing the crankshaft & vib damper & flywheel & clutch all individually and then all assembled.
VAC sells a very nice VIB Damper, which I may get soon.
But to aid your case, I ve been able to rev all day long 9000-9200 rpm with zero issues, and mine is a stroker 3,500 cc as well.
So the main source could be balance related.
1st get all rotating parts individually balanced
2nd get them assembled and then balanced as an assembly.
3rd buy an oem vibration damper.
E46 M3 Sedan All Wheel Drive Twin Turbo
0-100 km/h 2.91 seconds @ 15 psi
E46 M3 Coupe Turbo 60-130 mph 4,2 seconds (2011)