The questions that comes to mind are two:
Why did you pull it?
How does it run?
If the former is to gain access to 'stuff', please list.
If the latter is 'unknown', the pulling the engine without determining its condition might have been a bit premature.
If the engine ran OK, then just do the normal stuff: hoses, filters, thermostat using a (Stant/Motorcraft), plugs, wires. If there is cam cover or pan leakage, do those gaskets. If the rear main is leaking, {NOT seeping} replace that. Replace the timing belt.
Water pump is totally accessible w/o removing the engine, actually, so is the thermostat. If the cooling system has been maintained, there should be little to no sludge in the water jacket, so relatively nothing to do there.
If the clutch, pressure plate, and throwout bearing assembly are replaced, it would not be out of line at 200k miles. Be sure to get the correct throwout bearing for your vintage and transmission as there are multiple versions. Perhaps a new master cylinder would be appropriate as you will be bleeding the whole mess on assembly.
If you decide to take the engine apart and do internal work, a minimal pile of parts would include bearings and rings, standard size unless you have the crankshaft journals ground undersize or have the cylinders bored oversize, requiring new rings & pistons.
The lima will do 300,000 miles with little problem. Unless the bores are rusted, I'd leave things alone if compression was good. I think you want compression above 140psi, but that would be at sea level, more or less, and I don't know your altitude.
tom