Well...the saga continues, and the 'hair pulling' is for a little while (all depends on Murphy's law) over.
After more cutting and welding of the manifold (thanks again Chris for welding), and then having the flanges machined flat at local CNC shop, it is finally ready for pretty much final bolt on. There isnt much clearance to the rad, roughly 2cm (about .75" or so), but since the mounts are solid, nothing is really going anywhere. I also got all IC piping mocked up and in place. Just need to weld in the blow-off valve fitting.
Photo below shows the brackets used to relocate the wastegate actuator - it was not clearing the crancase venitlation lines. I have not decided yet if this is going to be internally wastegated, or externally wastegated setup. If turbocharger performs to the expectations, It will be converted to non-internal wastegate. For time being, external wastegate port on the manifold is blocked off.
Overall view
I also managed to put back the center console after installing the 'god-mode' switches.. IC sprayers, colling fan and the middle one is yet to be determined.. Above is the mini turbo timer, and E-O1 controller.
If I find my exhaust pipe (which is somewhere at the backyard of work and burried under snow), I believe I'll try to start up the motor next weekend.