1. I didn't recieve any footman loops either, not a big deal to me, all the bow packaging looked very good on mine, plenty of nuts and bolts and stuff, but no loops. Not a big deal to me, as my factory ones are still installed.
2. The windshield peice installs on top of the frame, not in the front like you have it. My 73 had factory threaded holes in the top of the frame. I just drilled my soft top peice and there it was. I suspect that 75 and up no longer had the holes, not sure. Up until 75, 40's came off the line with all the holes for either a soft top or a hard top. Only holes not functional are the holes in the dash for the door straps. As Liam put it, screws will work across the top as well.
3. Mine don't hit the tub holes either, but I measured and my rear bow is just over 1200 mm to the top of the bow. I'm going to tweak it a bit, shorten the legs for factory spec of 1200mm and then I think the rear flap opening will then reach better to the tub and the holes it should hit.
4. The smaller rear crossmember is wrong on mine also. If you look closely at all the bows where the fit together there should be stamped letters. Either X or XX. Match the letters and the holes will line up better. You either have yours backwards, or you have mine,

. The rear one over the door is stamped with E and EE, but the peice that slips on is stamped with G and GG. Thus the little holes do not line up, because they were not drilled together. So mine may be with someone else.
5. Answered above, I think???
Overall, I thought it all goes together pretty good, it just takes a little adjusting. but once you fit it up, it will be easy to take on a off. Like most things on a 40, it just pretty much bolts together, unlike newer vehicles where nothing fits again once you take it off.