While I have never used it, the body guy may have recommended POR15 which is supposed to be good for encapsulating rust. It is a great paint for sealing rusty surfaces.
I bought my needle gun at harbor freight and it has worked fantastic when I have used it and it was very inexpensive. Just beware, it could perforate thin metal...but if that happens it was probably in need of replacement anyways. If you only have a few rust pinholes, I would not (unless it is in a structural area) replace it. Instead, you can use a fiberglass reinforced body filler. You will want stuff with long fibers. It can be thinned out with polyester fiberglass resin to make it more spreadable. This stuff is waterproof so if you thin it and spread it on the inside, a little will squirt out the exterior through the holes and it will seal the floor. I wish you the best luck on the project.