Hello, I've got pretty rusty fuel injection pumps that I'd like to clean and paint. I'm considering using rust remover but wanted to check with you all before doing so. Aside from keeping these ultra clean and keeping pistons and barrels matched, is there anything else worth noting? I was going to disassemble them as far as possible as well. 
 
 

Still looking for some experts here, can anyone recommend any videos, articles, or instructions on how to tear down these units and then build them back up? I've taken measurements to be able to set them all back to their original settings (not going to remove the gear from the piston) but was considering removing the threaded bore. I'm also curious about what looks like an o-ring gland at the base of the pump - there is no call out for an o-ring here in the parts manual and there were none when I removed them. Given the amount of rust in that location I'm thinking a o-ring would be a good addition provided it doesn't interfere with seating to the pump housing.
I have read through the Servicemen's manual for the fuel pump assembly which centers on the housing and adjustments, but it doesn't talk about the individual pumps which seem to be considered a bolt on part. There is a small adjustment screw on the pump, is this a bleed screw or is it used to tuning?

there is a separate book for the engine and the fuel system itself it goes into more detail. tha screw with a flattend oval head is the bleed screw. the tool is available from cat except its a socket not a spanner chapter 19 does sell a reproduction spanner.

I would clean it up as best you can with a wire brush and spray it with a preserving film. Make sure you don't get any on the piston, bore or the pumps mating surface.
As long as the piston travels up and down in the bore smoothly there is nothing much you can do with them. They are an extremely precise fit and unless you are having issues I would not remove the threaded bore. As for the o-ring like groove, if there was nothing in it from factory then it probably shouldn't have anything in it now. I have removed diesel varnish on pistons before using 1600 grit sand paper but that is as far as I have gone with them.