I've also been told not to use silicone on a tranny gasket. If the silicon drips off on the inside you will have major problems with the internals of the tranny. If the pan is straight you shouldn't have to use the silicone. I had the same problem you are having. I pulled the pan and eye balled the mating surface and discovered that the spaces in between the bolts was lower than at the bolts. Once I straightened it, it worked fine. Has anyone used a screw driver to pry off the pan?

Good luck!