It is hard to tell in the pics. Is the seal flush with the case or even barely under the case? If so good to go.
To elaborate on the paint mark on the crank for the flywheel. The paint mark IS "supposed" to be lined up with the crank shaft rod pin.
If you TDC your LH piston, I do not care where the valves are at or the timing at this point! Just TDC with a straw, screwdriver or the like in through the spark plug hole and rotate the engine to find LH TDC.
Find the arrow on your flywheel. Line up arrow with the cast nub/pointer on the LH top side of bell housing as shown in your shadow pic.
Now, the bolt holes in the flywheel and crank shaft should be aligned, or "maybe" a 1/4 bolt hole off due to visual error. Adjust slightly to line up the bolt holes. TDC is done for the crank and fly wheel.
Hope this helps,
Tom