I noticed one of the items you were cleaning was the oil pump, and it reminded me to make sure you know that the gasket for that MUST be the correct thickness. The gear clearances are determined by the gasket, so your oil pressure will be affected if it's not correct.
Almost any other gasket on the tractor is not critical, but that one is.
http://www.tmtractor.com/new/en/258fp.htm
Also, have you tried using electrolysis for rust removal? It works quite well, though it takes a bit longer, but it is not as caustic... won't eat up your hands as fast! It uses a 12v source, with a piece of scrap metal and your part to be cleaned hanging in a tub of water with Washing Soda...if you do a Google search you will find lots of information. You can search here on the forum, too. Here is one result of a search:
http://www.myfordtractors.com/electrolysis.shtml
I use a large plastic garbage can and a 12v battery charger (non-automatic), and a mower blade for the sacrificial anode.