Locked and Loaded
Joined: Dec 2003
Location: Tallahassee, FL
It seems you took off down the wrong path. The effective way to fix it now would be take it to a body shop, and have them repaint the area, possibly the entire side. For future reference I'll give you some hints on what to do.
Don't use filler/primer on a scratch. You should have taken a high grit sand paper to the edges of the scratch to feather it out just a bit. The touch up paint would have worked fine if you would have used the pen tip to fill in the scratch. I know it will leave a raised area, that's fine. You should have then wet sanded the bump from the touch up paint down until it's smooth with the rest of the paint, and feathered it in with the paint ~2" around the scratch. You might have to use the brush to get a good fill at this point. It would then need a couple hours in the sun to make sure it's hard enough to polish out. I would have started with something along the lines of Scratch X, a diminishing abrasive. That used with a random orbital like the PC 7424 would make it extremely hard to notice, but take it a step farther with a good glaze and sealant with a nice coat of wax over the entire car. You'd be amazed.
I've fixed a key mark on my friend's Indigo metallic blue '04 cavalier in a day for right at 30 dollars for the touch up paint, and my use of materials. You'd never know it had a key touch metal.
95 Volkswagen Golf Sport - Low, slow, and loud purchased 4/5/08
93 Nissan Sentra SE 2 door - sold 4/5/08
88 Honda Civic DX Hatchback - sold 9/26/07
85 BMW 325e Coupe w/ 88 I motor swap - sold 2/24/07
93 Sentra XE 4 door - wrecked 7/29/06 totalled.
90 240SX Fastback - sold 7/15/05