[84LX89GT]

Well if you removed the camshaft position sensor (in the hole where there used to be a distributor) then you'd need to retime the engine which you have to have a special ford synchonizer tool (it's a plastic cover that you slide on top before installing sensor). I would clean off your engine pretty good and let it run for awhile.
--Make sure there's no coolant on the spark plug electrodes (the part that goes into the engine) because that will cause a misfire. Also make sure there's no tears in the spark plug wires.
Are you sure you installed the spark plug wires back onto the correct cylinders? that's an easy mistake to make especially if the spark plug wires have been replaced with non-numbered wires.
Sometimes a miss will go away after warming the engine up and sending all the crud left in the engine out the exhaust. I would start it up with the radiator level topped off to the full mark. If coolant is flowing out quickly before it's even warm or you see lots of bubbles in the coolant for an extended period of time you have a problem. Also if it starts to overheat that's a good sign something is wrong. I believe on those engines you can install the head gasket wrong and block off coolant passages which will cause it to overheat if that happens.
Another thing i'd look at is since you had the intake manifold off, running rough could be a vacuum leak. If you hear a hissing noise from the intake that wasn't there before there might be one. An easy way to check is to spray small amounts of brake clean spray at where the intake mounts to the heads, between the upper/lower intake manifold and at vacuum lines. An easy way to tell if it is a vacuum leak is if it stops running rough when you bring the engine speed up from idle to about 2000 rpm.
Good luck