You need to figure out the best place to see the marks. Sometimes I will turn them so they are facing down, and then lay on my back and look up to see them. You can then take some very fine sandpaper and run over the marks to bring them out. Once you get the marks so you can see them, it should be self explanatory. You should have a TDC mark, and then a series of marks with a BTDC stamped in on that side. That is the side you want. Most of the computer controlled engines were set a 10 BTDC, and most of them I have seen have a deep groove in that position. I would then get some whiteout, and make a mark at the 10 BTDC groove. I then usually make another mark but only half-way across at the 12 degree mark. This lets me know where I am at and if I want to experiment later, which way to go to advance or retard the timing. 10 BTDC will be good for now though.
I never had quite understood what is wrong with your starter. You said the holes in the plate between the engine and trans were too large. But the plate doesn't position the starter, the holes in the transmission position the starter.