Jon, i believe workshop manuals are still available from your AGCO/MF dealer.
When the Thermostart is activated it meters a small amount of fuel from a small holding cylinder in the "leak off" return line from the injector pump, this is then ignited by the heating element and drawn into the manifold, your thermostart sounds like it is likely burnt out and needs replacing.
The hydraulic filler is located to the left of the main gear shifter, a large plug, the dip stick is by your right heel when sitting on tractor, this is a common reservoir for the hyd/trans/diff.
If your 35 has the dual clutch the 3pt hitch will operate independently of the PTO when the clutch pedal is released.