Need help, dont know whats going on, misfiring? Options

[6GCBORO]

So im going to start out by saying i got an ebay header for my 1.8l about 2-3 weeks ago because of the old manifold cracking in multiple spots. We had it installed but no other exhaust piping was changed. (i do have a flowmaster exhaust though, dont know if that means anything.) So i drove it for about a week all fine. obviously somewhat louder and some rattling most likely due to something being loose or hitting against the undercarriage. Then about 2-3 days ago I started it up left the house and half way on my trip, it felt as if i was driving on a complete flat. no flat but went back home and on the way it just felt as it kept being pulled back let go pulled back let go. asked the mechanic, he said change the plugs. so i did. no change. then we adjusted the timing just a bit. I dont really know anything about that so i let them do what they thought. that stop and go/flat feeling while driving went away. NOW, i will drive and obviously i know my car and the clutch but it seems that ill let the clutch out a little to fast now and it will misfire just a bit mostly at 1st and 2nd gears sometimes 3rd. only when i let the clutch out to fast which isnt fast at all since i tried going slower. But in 1st and 2nd gear it will misfire a good amount going up some small hills. once i get speed going though im relatively fine. Everything before installing the header was fine so thats why i included all that. the flat tire/pulling feel and misfiring started when we dropped into low temperatures here in new england. just some xtra info.