Good afternoon
Try search on your individual questions. The following I what I have done for the Thunderbird Super Coupe. This is just an overview. I mean no disrespect if I omitted anything and did not go into super detail.
PHASE I Getting ready.
Research . Start with SCCoA. Get a service manual, Chilton and or Haynes. Have a good set of hand tools, large "1/2 drive breaker bar, and torque wrench(s). Special tool. Torque angle/degree indicator. Drain pans, Jack stands, work light, sandwich bags, masking tape, sharpies, anti seize, oil and filter, anti-freeze, supercharger oil, and sealants. Lots of rags/shops towels and large lawn bags including a note book. Decide on gasket kit manufacturer and if you want head bolts or studs. You do not have to de-service the air conditioner.
I think you get the general picture.
PHASE II. The Disassembly.
Draining fluids. VERY important. Drain a small sample of engine oil and put it in a cup. If the oil is milky chocolate and or full of anti-freeze you are taking a risk the bearing have been saturated by anti-freeze and may fail during engine operation. If the oil is dark in color not milky stir to check for silver bearing "sparkles" raising to the top. The bearing are shot. Engine due rebuild and or replacement.
Remove the following:
Battery, accessory belts, accessory bracket, exhaust manifold, electrical connectors, harness spark plugs and wires, vacuum hoses, valve covers, intake duct, radiator, fan, and hoses, supercharger and tubes. Everything address in SCCoA forums, service manual, Chilton and or Haynes. Finally remove the rocker arms, push rods, head bolts and heads. Make sure you take pictures and or careful notes. You will thank yourself later. Bag and tag everything. Put parts in trunk and or back seat.
PHASE III. Inspection and Potential Parts Replacement.
Send heads to machine shop. Pressure testing, valve guides, seals and resurfacing is a must. Sends radiator to be pressure tested. Have the alternator tested. Have the starter checked. If you need a battery now is the time to get it. Change the fuel filter. Clean the MAF sensor. Chase all engine block to cylinder head bolt holes and air dry. Make sure there is no traces of gasket material on the block.
The below are items that if not checked has caused me grief because the car had be out of service and was much more accessible.
Power steering rack.
Power steering pump, pressure and return hose.
Throttle body TV bushing.
Upper and lower control arms.
Tension struts.
Inter and outer tie rods.
Stabilizer bar link and bushing.
TEVES II unit. May need replacement accumulator ball.
Engine and transmission motor mounts.
Bottom of oil pan for sever power steering rack line rubbing.
Coolant hoses.
Radiator cap.
Supercharger for low oil. May have to change nose seal.
Clean carbon build up EGR passage at the intake plenum. Locate and match 2 raised head bolts at the hardware store if the EGR came with non raised OEM bolts.
All three belts.
Harmonic balancer bolt and washer if not previously change. Check for cracks in the rubber.
Harmonic balancer to Timing cover seal.
Water pump.
Thermostat.
Radiator fan connector.
Repair or replace thermostat housing (flange).
Oxygen sensors.
Oil sensor.
Oil pump.
Coolant sensors. Engine and Gauge.
Motorcraft PCV valve and valve cover seal.
Heat sink for the DIS.
Spark plugs and wires.
Battery cables.
Ignition switch in the steering column.
Electrical tape and various sizes of split loom for harness repair.
Hard vacuum hoses ("5/32) and connectors for HVAC repair.
Buy or rent a tap and dye set and chase all bolts.
Make sure you have the cylinder heads dowells or replacements before you turn in the heads to the machine shop.
PHASE IV. Corrosion Control, Clean and Paint.
Clean the engine bay. Correct corrosion issues such as accessory bracket, pulles, exhaust manifold, and accessible grounds.
Touch up paint as necessary. Look especially under the battery tray.
PHASE V. Re-assembly.
Inspection and repairs on individual components are completed at this point. Re-assembly components. Again SCCoA , manuals, picture and notes are your guides. NOTES.
Before assembly of the cylinder head chase the exhaust manifold and valve cover thread holes. There will be debris.
Don't forget the dowels.
Use the torque degree angle to insure consistent torque to yield cylinder head bolt stretch.
Following instruction from ARP for head studs.
Use electrical cleaner and finish with die - electric grease inside the connectors.
PHASE VI. First start.
Service radiator. Add engine oil and filter. Add power steering fluid. Give a very through visual inspection. Disconnect coil pack connector and crank over engine until you have indicated oil pressure. Re-connect coil pack connector. Start engine. Hopefully the intercooler tubes are sealed tight. Check for leaks. Check for Engine check light, coolant servicing and fan operation during run. Bleed air from power steering pump. Shut down. Check oil. Might take a while to bleed air from the coolant system so what I do is leave the car on jacks wait a few hours and restart.
PHASE VII. Road test.
Take car off of jacks. Drive car. Checks oil, anti-freeze and power steering levels. Adjust and or correct as necessary.