As my van was a passenger van for most of its life there was 3 bench seats and the remnants of a wheelchair lift. All of which had to be removed for the flooring and insulation to be installed and with that was going to come holes in the floor.
After all the brackets were removed and the bolts cut off (most were rusted) I was able to remove the wood flooring that was below the factory rubber mat:
After that I had a rusted floor with a bunch of holes in it:
So sanded down all the rust, which took a while. I am a fan of using an angle grinder with sanding and grinding discs. Its really loud and makes a mess, but makes quick work of rust and burrs.
After all the rust is removed I used both my cheap Flux-Core welder (NOT RECOMMENDED, cheap welder made too many holes) with steel sheets cut with airline snips from a sheet like this. When the welder didn't work great I just epoxied the metal sheets over the holes to seal them using Loctite Epoxy, however I have since used PC7 Epoxy and like it much better, way less runny that Locktite.
Once all the rust was removed and holes epoxied I coated everything in POR-15. I cannot speak highly enough of POR-15. I have since used that on all rust issues. With that being said prep work is the most important aspect of using POR-15. Do not skimp on the metal prep, I bought this huge bottle of it and really glad I did. You can tell when it etches the metal.
Make sure you do research on the process as its multiple steps including washing the surface down with water (which is odd to me). I watched this guys video to help out as he also uses and angle grinder in the process.
Once the POR-15 was dried I applied some rattletrap, but it was unneeded as I ended up spray foaming the vehicle anyways. But I figured it cant hurt, keep in mind its not cheap though.
Since I had exposed a lot of bare metal with the grinding and cutting of all the bolts and brackets that went through the floor it was really important to make sure the holes were sealed up on the bottom and the bare metal was treated/coated/painted. I used epoxy again to help seal up the holes and keep water out. Once that dried I used a rubberized under-body coating to cover up the bare metal and prevent future rust, in hindsight a primer would not have been a bad idea...
Next step would be insulation the van, soon to come.