99 4.0 OHV miss

In the process of replacing my timing cover and gasket I also noticed that I had a small leak on the lower manifold gasket so I removed the lower manifold and replaced with a new gasket. When I started it up I noticed that I had a slight miss. When I took it apart it was running fine just the water leak and I now noticed that I get a sulfur or gunpowder smell that I didn't have before and when I hold the rpm's at 3000 for a while it will climb up to 4000-4500 rpm's and then back down. No codes have been set but still have the miss. I checked the plug wires and plugs all ok, the compression was 185 on all cyl. and as far as I can tell all my connections are plugged in. Any ideas what might be causing this miss? One other thing I forgot to mention was when I tryed to start it for the 1st. time after the assembly I had gotten the no. 5&6 wires crossed so it bucked, coughed, and spit but would not start. Could this action of caused a push rod to get bent thus resulting in a misfire?

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1999 Ranger 4.0 OHV, xlt, 4x4, auto,

Push rods are all OK.

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1999 Ranger 4.0 OHV, xlt, 4x4, auto,

I'm not familiar with the term 'lower manifold'. Do you mean the exhaust manifold? , or the lower intake manifold? I'll assume the intake. Sounds sorta kinda like a vacuum leak. Check your vacuum.