Yes. Those pens are really not meant for very fine work. If it is not too late, try putting some of the "paint" on the tip of a needle for very fine application. You might have to apply a couple of layers when using a needle. Just let the previous layers dry for 10 to 20 minutes before putting more on.
After shaking up the pen, I made sure that I got a good supply of metal-laden paint by dabbing the tip on a paper tower first then tapped the tip with the needle to get some on it. When my mod. didn't work even after all these steps, I went back and actually soldered mine as I saw that it wouldn't matter anyway. If your mod. works then you MIGHT want to consider a more "permanent" bridge.
If you can manage it ( it is very fine work -- loupe and tweezers a must here ), try putting some masking tape around the area to keep stray paint from getting on the other traces. I didn't do this since I didn't expose any other leads close to the dots. You'll need to pull up the tape as soon as you are done applying the paint.
I think an hour of open-air drying is enough, but a lot of people wait the 8 hours because it seems to work. It won't hurt to put the card back together and install it after some open-air curing time then power up long enough to check it. If the mod. worked, then power it down and let it sit overnight to finish curing.
About scraping ... Even the smallest flat-head screwdriver from one of those six-piece precision kits looks HUGE next to those dots under a loupe. I used a screwdriver that is in a watchmaker's kit.
This is probably WAYYY! too much that you want to pay for a screwdriver set, but this is the set I have ... http://cgi.ebay.com/Bergeon-Screwdri...QQcmdZViewItem
These ( http://cgi.ebay.com/7-Pc-Super-Preci...QQcmdZViewItem
) might be OK, but I don't know what the blades look like under a loupe.
I also have loupes like these ... http://cgi.ebay.com/5X-10X-15X-20X-3...QQcmdZViewItem
The 5x, 10x, 15x combo loupe is cheap plastic but does the job. The 10x - 20x is a decent metal one but the viewing area is pretty small. The 30x is a little overkill but it will clip onto a Helping Hands tool for hands-free magnifying.