Using a file on the floppy drive hole should work fine as long as you don't use too much force, try to hold it in a sort of horizontal angle in order to file over a wider area. But before you start making the holes, you should probably find a way to mount the floppy drive properly first.
Regarding the expansion card slot, I don't think you will find any adapters for your needs, so you probably will have to make your own. But if you do this, it might be an idea to try making it as short as possible.
I don't know what your HDMI board looks like, but an idea could be to buy a short HDMI extension cable which have screws included on the connector, there simply must be something like this to be found on ebay.