What are these holes in the floorpan for? Under the holes marked with numbers 1 and 4 you can see the bracket for rear swingarm. If they are supposed to be plugged, how can it be done because the bracket is partially blocking the hole? What is the use of holes 2 and 4, should they just be plugged also?

TpT said:

What are these holes in the floorpan for? Under the holes marked with numbers 1 and 4 you can see the bracket for rear swingarm. If they are supposed to be plugged, how can it be done because the bracket is partially blocking the hole? What is the use of holes 2 and 4, should they just be plugged also?

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Holes 1 and 4 are redundant and it looks like they are there because the strengthening fillets were not handed in manufacture in order that one pressing worked on either side.
Hole 2 is for a rubber hold-down rivet for the floor covering; there's similar one on the other side. Hole 3 looks like a random, non-factory drilling.
You probably have carpets so they could all be filled with sealant or blanking plugs. In the UK models these would all have been covered with thick sealant from below but you will have had a replacement floor.
See photo of my car when stripped-down.

If the holes are not required, I would suggest that you plug them with rubber grommets---they are available in a large size range. Measure them, then obtain a (free) catalogue from "Car Builder Solutions" (if you are in the UK)--page 396