If you have to do the headgasket and small ends I suggest dropping in a good EL motor (hehe or AU hehe)
Should cost about $700 for the motor, although if you don't DIY labour costs could be a bit high - having said that paying somebody to rebuild the old motor won't be cheap either.....
Thermostat is cheap and easy, I'd do that first at $20 or so if I were you :)
And if you want a 5-speed anyway, why not wait until you can afford it and do both the box and the motor at the same time? The 5-speed and 3-speed wiring is exactly the same, whereas the 4-speed will require rewiring to suit.
The motor should last you a few k's yet if you do go that route.
Anyway, my 15c
Proud TQE Operator and President of SEFAG - the Society for the Elimination of Ford Automatic Gearboxes
Pacemaker headers + 2.5" exhaust
EF Fairmont interior
Lowered King springs
5 speed manual
Newest mod: EF Ghia wiring loom and dash