Patrick,
Well, you will have to make some sort of hub for the flywheel end to attache a degree wheel to, in lieu of having the flywheel fitted. The flywheel does make a handy thing to tape the degree wheel to, or for marking out degrees with a felt time marker along the rim. I presume you want to leave the timing side clear to allow arranging of the timing gears. It is easier to determine TDC after the cylinders are fitted. But there are two ways to determine it without. One is to use the keyway on the timing side of the crankshaft. This points to TDC on a cylinder. However it is hardly worth the difficult task of extracting the pinion, if it is still fitted. Nor am I sure how you can utilize it as an accurate reference; it is typically used as a visual reference (which cylinder of to fire). The other is to use machinist combination square off the face of the cylinder base joint, You need to reference the machined slot on the crankshaft throw that is used for the extractor to dismantle the crankshaft. Or off the side of the center web. Both these are parallel to the plane of the crankshaft throws. In theory. Not having tried this, I cannot say there is enough room to pass something into the crankcase alongside the crankshaft.
-Doug