well. i think you've set yourself up for alot of potential cracking in your finish with all the bondo. What you should do is sand everything smooth WITHOUT adding more bondo. All you should have left in the end is a thin pink line where the bondo is briding the gap between screen and bezel. Start with something coarse like 180 grit until you hit the original plastic. Then move to 220, then 400, then 600.
The next thing i would suggest... and i CANNOT emphasize this enough, is to get a sanding block. You can get these at auto body or paint stores for CHEAP... like $1-5. It's basically a soft foam/rubber block. When you wrap sandpaper around it, it spreads out your finger pressure so you get smooth even surfaces with no waves.
When you're ready to repaint, use the proper primers and paints. If you're not going for a "class-A" paint finish, look at plastic specific paints. Krylon Fusion paints should be easiest to find. If not, the Duplicolor paints at Wal-Mart, Kragen/Pep Boys, etc... will suffice, but you SHOULD look into an adhesion promoter like Bulldog to spray on before it.
That should get you a little further than you were. As for your fans... i'd look for a vent that you like that fits in the space and mold it into the space in the same way you did your screen. Then just use simple duct tubing to connect your factory ducts to the vents. The other possibility may be to trim the vents you have... cut a section out and reglue it together so it fits.