You are experiencing the same weatherstrip problem I had then. If you can gently remove the weatherstrip and align the door you'll be better off in the long run. It seems like that would take longer but it's probably your best bet. Use a forked tool to pry the plastic push clips out of the door so you don't tear the rubber molding. Align the door and then install the seals.
When you reinstall the rubber you'll find that trimming the section of the upper front (by the cowl) on the backside (where it touches the door)so that the rubber contour matches the contour of the door sheetmetal better will make a huge difference. Also you'll probably want to trim the rubber so it doesn't stick up above the door in the little corner (you'll see). Once you get it contoured to the door so the door doesn't bind when you close it and trimmed on the top you'll need to glue it in place with 3M weatherstrip adhesive.
The upper rear end of it also needs to be trimmed on the back to get the gasket to stay along the edge where the last push clip is. 3M adhesive needed also here.
If you bought the window rubbers as well they also have fit issues on both ends. Start by installing the vertical part then work across the top and down the A pillar then trim the ends on the backside to the contours of the sheetmetal. You'll notice the original piece is made of much softer spongy material on the A pillar end. It is hard to get the new part trimmed to not cause bind so don't glue it till you're sure.
I took this pic when I was doing mine to show the difference in the way the new part is molded compared with the original. The fact that the new part is made with a much harded rubber compound makes it worse.