First, I'll assume that you are going to leave the floppy port unless you want to take the chance that you can cut that section out and be able to get a multi/reader/USB there without leaving a gap or open space in the bezel. If not I hope that blank right above it will come out.. then I would leave the floppy port there and just utilize the mount above. Problem is where are you going to put the HDD.
There are so many problems here not sure where to start. Is that plate attached with rivets or screws? Either way I would guess that the reason you can only get 60mm in there is because of that plate. If it won't compromise the integrity of the unit I would remove the plate so that I could at least get an 80mm in there. Second problem is that I don't see any standoff positions in there on the case side for the MB. Unless there was a plate that came out of there, mounting a retail MB is going to be a real pain.
That should be fine, although the clearance with the PSU because of its position may make it somewhat ineffective except as an intake fan. You might be better served to put that fan in the lower front portion of the panel. Also, be very careful with your cut here.. the metal liner in that side panel is extremely thin. If you have access to a drill press and hole saw, drill from the metal side with a wood block under the panel.
Here is another place that is going to create a problem. If you retain the stock position (assuming that this plate accepts a standard ATX type PSU and I don't really see any way to change that) it isn't going to leave much space underneath there for the CPU cooler. The only other place to mount another exhaust fan would be in that plate behind the drive bay above the PSU container. Can't tell for sure from the photo but it doesn't look like you will get much more than a 90mm in there. The only other option is to cut in the top for a "blow hole" right above that same plate.