a727 no third gear

Well, if you found an issue in the valve body, I would think you are gonna go back there first! Maybe try a known good one and go from there. I would not be a bit surprised to find you have a fried rear clutch, even if it looked good before. Just because it sounds good does'nt mean theres any frictions left. BTW, where did all the fluid go?? If you are saying it leaked out whilst someone was driving the vehicle, well then there is damage done!
the truck saat for a long time 10 or 15 years not sure, but the trans was empty, all the clutches front and rear were practically brand-new, there was no friction material or any sort of debri and the filter didn't look nasty at all when I did drop the pan.