I have tried everything to get that crap off the area so I can do a proper repair and hope some one has a method because I know that nothing will allow epoxy and varnish to stick

Nick:
Good to hear you are 'on the mend'...I hope you are back to 100% real soon!

About silicone...I know the problem.
I'd start with a sharp (carbide or cabinet) scraper and remove as much silicone (and probably some underlying varnish) as possible. Leave any sanding till the last, as it can just carry the contamination further into the surface.
One product that seems to do a reasonable job (I use it) removing silicone wax is Interlux Fiberglass Surface Prep
http://www.westmarine.com/buy/interlux--fiberglass-surface-prep--P014145270
It seems to be a detergent product with an abrasive. Definitely not a high VOC solvent type product.

Silicone contamination from car polishes and waxes is a known problem for auto body guys, so a local auto supply shop may have some similar products, or solvent 'washes' for removing silicone. If you could spray a finish on it without fisheyes, epoxy would probably stick to the same surface.
My latest silicone story (possibly a repeat, sorry..):
A couple of weeks ago I was removing an old 'camera mount' from a kayak deck. There were screws driven up from under the deck, but I didn't realize the previous owner had smeared silicone over a wide area under the deck - probably 'cleaned up' extra silicone around the screw heads with a rag and paint thinner. I put on a glass patch with peel ply after giving the deck underside a 'good' hand sanding with 80 grit paper. Next day I yanked the peel ply and off came the entire patch!
It was a good (Mariner) glass boat which had been built with roving and vacuum bagged, so there was a lot of texture inside the boat. It was a real 'pain' to clean up enough to patch properly.