ChrisG: i just installed a Yakima rack with control towers a few weeks ago. I removed the gutter covers (start at the rear of the car. Open the hatch. At the very end of the plastic strip, you will see a small cap/thin line before the strip terminates. You need to use something to push this clip backwards, towards the hatch. Either the strip, or the clip will move backward, approx 1/2inch. Once it has moved, use a cloth covered screwdriver, and lightly pop the end of the strip near the back of the car, up. There are 4 points along the strip where it clips in. If you're having trouble, hold a section of the strip you already have popped up, and pull it slightly back towards the hatch. When the strip no longer moves, continue popping until the strip is completely removed. This is INCREDIBLY easy. You should have both strips off within 5 minutes.
I then drilled holes where the mounting bolts need to go through the strip, and installed the rack. Easy.
An easy way to drill the holes in the correct location: Take a very small piece of paper towel and twist it up, insert it into the mounting plate. Apply a small dab of grease to the top of the paper towel twist. Reinstall the rack being careful not to toch the grease until the gutter strip is in the correct position. Where the grease marks are, is where your center is.
Note: Even with drill bits rated for metal, the odd make up of plastic/sheet metal will twist and bind a bit during drilling. This won't necessarily be a super clean install unless much time and the proper tools are used. However, it didn't bother me as I was installing the rack for good, and the $120 for the strips with removable slots was an unnecessary expense.
Lutexas, I did the same thing when installing my Yakima control towers. As it ended out installing the rack on my car, the allen bolts threading into the plates never got tight. The control towers did, and even began to slightly indent the roof (not permanent, yet anyway.) I tightened the allens down until the roof just barely began to compress slightly (noticeable under garage lighting.) The control towers themselves, do not twist or rock, but the bolts are far from what I'd call tight, (1/4 turn past finger tight basically.)
As for the plates, depending on how far they bent, they can be repositioned enough for a clean install. I used a steel hammer, and a punch. I placed the striking surface of the punch, onto the top of the threaded barrel of the mounting plate, and over the course of 5 minutes, made short, yet firm strikes down on the punch. When I was finished, the mounting plate was maybe 2-3mm above it's original state. Good luck.
Apexistud, thanks for the post brother. I'm going to check up with that company in an attempt to acquire some mounting plate spacers.