That video was painful to watch.
The assembly steps were pretty straightforward, but some of the tools and techniques used during the assembly had me shaking my head. /ubbthreads/images/graemlins/banghead.gif
And not a damn thing mentioned about balancing the components, rotating assembly or the center cartridge.
As for using a carbide bit to clearance out the bearing housing deck to accommodate a larger thrust collar, you should be alright as long as you take it slow, don't remove any more material than you need to and make sure to thoroughly clean the bearing housing out afterwards. The only area you want to pay attention to while removing material is to ensure you don't remove material from the bearing housing that feeds oil to the thrust bearing.
It's not a critical machining operation, because all dimensional clearances for the rotating assembly are maintained by the pressure from the nut compressing down on the compressor wheel, thrust sleeve, thrust collar and the machined step in the turbine wheel. The rotating assembly is located in the housing by both the machined step in the bearing housing for the oil control ring on the turbine shaft, and by the thrust bearing which lays flat in the machined step of the housing. This ensures everything is properly located and should be unaffected by the removal of material from the bearing housing, so long as only the required amount of material was removed.