91 f150 4.9L no visible timing marks, hard start runs rough.

I have wondered why this happens many times in the past. You would think the marks should line up using #1 cylinder but they don't.
It has been a while but I think if you hook up to #5 ignition wire the marks will come up for you.You will need to undo the "spout" connector before setting it to 10 degrees before top dead center. The spout is a two wire jumper clip that should break out of the harness at the distributor.
Warm the engine up for a while so it doesn't stall as easy while you set the timing.

There is one set on the right hand side near the top of the timing cover, these marks are cast in the cover. These naturally are the WRONG marks. On the left side of the timing cover where you can't see them are the right marks. They are on a metal plate bolted to the cover using the cover bolts. The vibration damper also has two sets of marks, wouldn't you know it! There is a large square notch , nope not the right one . There is also a very thin scribed line on the damper, yep that is the right one. .
To do this right, slide under the engine and clean off the thin scribe line and paint it white and while you are under there you can see the bolted on timing mark on the cover there is a large triangle cut in the plate , that is 10 degrees before TDC the correct setting .Pull your distributor cap and crank the engine until the rotor points at number one cyl on the cap.Then see if you can see the alignment of the timing mark on the damper some how and the mark on the bolt on plate, its easier when the engine isn't running and you can stick your head in there without loosing half of it. Your timing marks should be some where near each other. Crank the engine to align the 0 degree mark and the mark on the damper, don't worry about the distributor position. Just line up the marks. Then go to the right side of the cover with the cast in marks( that you can see) and mark the damper with white something, paint even whiteout works.Now you have a new timing mark that you can see. Pull the spout, yes it is in the same harness as the distributor connector, its a gray jumper.Put the cap back on. Start the engine and use your new marks to set the timing at degrees before TDC.

Manifolds/gaskets go bad on this truck, usually have to replace both due to excessive exhaust manifold leakage & intake manifolds sucking vacuum. They warp badly, you're REALLY gonna love finding & replacing the emission pipes on the head. use LOTS of WD40, real 6-point pipe fitting wrenches, a small hammer to tap lightly with to aid in loosing & not busting these bloody pipes, LOTS of patience. parts , lots of parts. back to the Timing Marks, CLEAN all the front off, locate the Marks on crank pulley first & mark 0 TDC long line , 10 before or what half line, with white old style White out is fine. There should be a Hole for a factory Timing Probe & near that Hole , a Timing Pointer or Mark on the Timing Case. Highlight it withe the same White-Out. adjust as required