Hyundaitech, 99 Elentra rough running woes

The car had overheated while idling on an otherwise cool day. A fan on the cooling system had not worked for ages and this hadn't happened so I thought maybe the water pump had failed - and it was about due for a
replaced timing belt. I started it up later and it ran fine (smooth, etc). I did the following: 1) Replaced the plugs - it was long overdue. 2) Replaced the valve cover gasket... starting to seep. 3) Replaced the timing belt. 4) Replaced the failed cooling fan. 5) Replaced the lower timing belt cover - old one cracked trying to put it back on.
It sat without running for about a month. Started the motor and it ran rough and at first it made a taping noise like a little oil starved. Now just runs rough like misfiring.
Plug wires look fine.
I had used the mark near the crank gear. The cam sprocket has both lines AND a hole that had been lined up. I did take it off to replace the slightly leaking oil seal, but put it back on and lined it back up before installing the belt.
I had rotated the motor 2x and the timing marks had stayed in line. MAYBE the belt is a little tight. NOW I can't see the TDC indicator on the cover unless I take off the AC belt. By the way, the TDC cover mark was accurate - when I'd removed the cover the mark on the case was perfectly aligned too. So in all likelihood is the problem that I somehow was off by a tooth on the timing belt?
I need to get this car in good running shape for my son in Chicago who is starting teacher training this summer (before I move from Dallas to Tucson, AZ) HELP! Thanks. KWW
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If the engine runs rough even when cold, it's unlikely to be a timing belt issue. Depending on the severity of the overheating, the cylinder head may have warped.
You may wish to do a compression test and cylinder leakage test.
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On 6/20/2013 12:12 PM, hyundaitech wrote:

issue. Depending on the severity of the overheating, the cylinder head may have warped.

k thanks. It was very odd that before I did the work - after the engine initially cooled down it started and ran fine for < 1 min as moved the car in driveway on 2 separate occasions.
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On 6/20/2013 12:34 PM, KWW wrote:

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If the timing belt is too tight, you'll typically hear a whining noise from one of the timing belt pulley bearings. It'll change frequency with engin e rpm.
It's not uncommon for the oil pressure in the lifters to bleed off after si tting that long without running. Have you driven it yet? If not, and it's otherwise ready to drive-- especially the oil level needs to be okay-- tak e it out for a few miles and drive it real hard. Keeping the engine rpm up will help increase the oil pressure to the lifters.
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