If you've got some basic tools (sabre saw, snips, files, hammer , vise), get yourself some scrap aluminum sheet and have at it. It is fairly easy to cut and form all kinds of shapes to fill these larger holes.
Also, for the smaller ones, your local ACE Hardware likely carries plastic plugs in various stock sizes. I've found a number of uses for them, and their weight is almost imperceptible. You just need to measure the holes and buy a handful. Fit does not have to be perfect because the plugs have little expansion lugs built into them, and you can use sealant or weather stripping cement if you need air tight seals.
Here are some examples from my battery relocation and heat-delete projects:
I rerouted the starter cable and fuse box power supply through the large round air duct and made a cover plate with some openings for the cables.
The plate is about 3/32nds aluminum sheet. The plugged opening is for future use, and the plug is one of the above described Ace plugs in a grommet. The plate is glued to the inner flange of the duct with 3M Weather strip adhesive. It holds and seals well, but is easily removable.
Here is an example of closing the openings where the heater/defroster tubes used to be:
These were made from the same 3/32nds aluminum sheet, and are also held in place by weather strip adhesive. The upper one, directly under the wiring harness, is formed to the body contour, but it was very easy to do because of the pliability of the aluminum. Just press into place really.
Here is the battery mount for the smugglers box, again made from the same material:
Also, cut-up manila file folders make great template stock.
Good luck.