Rough idle after replacing alternator (??)

[Mammoth]

So it's been a week, took a drive on the highway for about 40 minutes of just straight driving time and she still running alittle rough and I'm running out of options I can't think of anything else. heres what I've done.
Had codes read (no codes)
Cleaned MAF sensor
Double checked Batt/alternator
Sprayed carb cleaner around vaccum lines (no rpm increase)
Throttle is functioning properly
Checked belt and pulley
Completed Drive cycle for ECU
Added some Lucas Fuel injection cleaner

I keep thinking I might of made a mistake buying an alternator that wasn't for this year vehicle (03' instead of 00') but I don't know how much that matters especially since it checked out fine. Just to explain it's not running horribly bad there's just a little loss in power and it doesn't idle as smooth as it did before alternator change.

 

[AbbadonTD]

you may have a bad relay somewhere, so that its working and sputtering. I wish I had a better answer than "somewhere" but it could be outside your alternator.

 

[Mammoth]

I talked to someone from Ford today and he told me to check my PCV lines/valve. That'll be the next thing I check. It's just frustrating!!!