What in God's name have you got yourself into here?
Probably more importantly why do you not have the complete Front Cover for at least one of these cases?
That Bottom cover shown in the picture should have a filter in it to stop air born crap getting sucked into the case. It's a flat Plastic Filter with a fine mesh on it that goes between the case and the front Panel.
As for the different Floppy Drive Opening in the case I would be looking at moving the Floppy into a space where it can be used ideally into one of the 5.25 Drive Slots with the aid a 3.5 to 5.25 Adapter.
Antec made flat Plastic covers that you pulled as required to fit external drives and you just bung those into the unused External Drive Slots/Holes.
The Metal Plates that Antec used where to allow the case to be a Full Faraday Cage/Shield to prevent RF entering the case and doing any damage so they quite rightly had holes in them as a proper Faraday Cage doesn't require solid metal to stop any RF.

Also the Black Optical Drive is incorrectly fitted as it should be as far out as the Cream one. Just in case you didn't know the Bottom Plastic Plate goes on First and really should have both Plastic Clips working to correctly locate it. You slide the Bottom bit up till it locks in. Then with the Top Plastic bit it swings on after you clip it in the Right Hand Side then just push the Left Hand side into place. I do seem to remember that the Floppy needs to be out quite a bit further than it currently is as well it should be level with the top Plastic Cover and these where a
tight fit. Just don't forget to push in the Lock on the Top Plastic Cover to lock it into place as you push it on. On some of those Antec Cases you needed to push the Top Plastic Bit on sort of straight to get it over the Floppy Drive and then drop the Right Hand Side into place followed by the left hand side clip. Also it's a good idea to take the side covers off before removing the Top Plastic Bit the Left Hand Side Cover should have a Lock and a Latch in it which you just pull up and swing out. The Right Hand Cover is located by 3 screws which could be Phillips or Thumb Screws like those used to hold the Floppy Tray in place depending on the model of the case.
Also some of those cases allowed you to slightly move the Floppy Drive Tray slightly by leaving the 2 Thumb Screws slightly loose to allow the Top Plastic Bit to fit correctly. You had a bit of movement between the Floppy Tray and the main Case which allowed the Floppy Tray to move left and right.

Also while I wouldn't recommend this, I have seen several people paint the entire case plastic and all with Lead Free Acrylic Paint from a Spray Can to overcome the different plastic colors that are so common now. Seems that they didn't like the Black Plastic Front Panels of the Optical Drives in a cream case.
Also for your Video card I've never heard of a PCI/AGP Video Card but you will need to install all of the drivers. The only ones I have ever used where PCI, AGP and then PCI Express all of which have different sockets and they can not be fitted tot he wrong socket.
There however may be some low end Video Cards made which suit either PCI or AGP which are interchangeable but to date I've never heard of these things existing. However that could be because I don't deal with Wholesalers who deal with that type of thing.
If you need the Plastic Drive Covers drop me a line I have heaps of the things here and I can post you what you need.
Col