My '71 Swinger is virtually rust-free, with the exception of some areas under the vinyl top. I removed the top and took the area down to bare metal. I tried poking a small screwdriver through every one of the pits, and while most areas were solid, I ended up with about 12-13 small holes.

This is the repair area on the passenger side...

Since these photos, I have welded the smaller holes, and made some small patches which I welded in to fill the larger ones. Now I need to contour the welded areas and prep the areas, but what's the next step?

I want to make sure the rust doesn't come back in the small pits. I have Metal Cleaner, but it is corrosive and I don't want to damage the original paint on the other parts of the car.

Any suggestions?

You could paint the area with rust stop primer - I like Eastwood rust encapsulator. A brush would be fine with your orignal paint masked off. Let dry thoroughly and use some spot filler to smooth the pits. After the spot filler is dry and sanded smooth, hit it again with rust stop primer. Optional, but I would give it a final coat of enamal to seal and protect.

Ive read that Rust Encapsulator does not adhere well to bare metal.

Should I use the R-E on just the pitted areas, then use POR-15 on the clean metal? Confusing...

I want to do this job right, and only once.

Welding the holes is fine...Ideally you'd want to spot-blast{as in sandblast} the badly pitted area to insure the rust is completely gone inside and out but I understand what you're doing...Weld,grind, then skim-coat the area with a waterproof filler...A smooth,fiberglass filler like marglass or a product like all-metal is waterproof and are excellent choices...All-metal is tough to sand though...
I've used Eastwood's rust encapsulator also{used to be called corroless} and have had great results{better than por-15}...And it can be used over bare, even rusted metal even though you really would'nt want to do that in this case... Here's the link to make sure everyone is on the same page{ } rust encapsulator