That brace in your first picture to the back of the hinge pocket is going to be in the way. Also it appears to be an attempt to hold the floor in position. I don't think that's really necessary, as you can locate the floor at each A pillar and make sure it's flat all the way across. You should also install some diagonal bracing across the door openings and at the A pillars across the front. Otherwise it looks like a good start.
For locating the floor, you can use dimensions from the FAM from the upper hinge bolts (or some other known point) down to the floor. Mark the A pillars at the floor elevation to give you a reference for the new floor pieces.
Got to get up early to get one past you! Yes, you are absolutely correct that the large tube bracing at the front will be in the way. That has ben there for 3-4 years and I simply haven't gotten around to removing it. Re floor height I measured from the first MGF hole at the top of the drivers door to the floor pan and it ALMOST matches up to the FAM at 44.96 (mine is more like 44.85, so I will recheck as the new panel goes in).
Thanks on the diagonal recommendation.
