There are a number of ways to skin this cat. I was having a similar issue when I did the skeg, so I elected to scribe the profile and fit a filler piece, which I found faster and easier. I wouldn't worry about gaps, though I would grind down bumps to eliminate as many as practical.
You do need to make a decision about bedding or bonding the skeg. The two are different and one doesn't need the other, if it's glued. I like to think about repairs and replaceability, so I went my way, but you may have different ideas or needs. Both a bedded or glued skeg can work just fine. Once the decision is made, you methods are the same. If you do glue it down, yep, watching for too much ooze out, from excessive pressure is a good idea. You can very slightly hollow out the underside of the skeg (where it lands on the hull) so there's a place for the goo to live, when bent into position. You also don't need fasteners, if you're gluing it down. Some weights will hold it in place until the goo cures. Rachet straps, Spanish windlass, even duct tape will do.
Don't use drywall/sheetrock screws as temporary fasteners. These will just piss you off, when you break them in the work. Use "deck screws" which are often coated gray. Also "tech" screws are handy to have a round too, with their button heads and point options. Both of these are much stronger and though slightly more costly, you can trust them to not break and they can be reused, repeatedly. I've found the drive type makes little difference if you're not asking too much from the fastener. A stripped out fastener is a pain in the butt, though you knew long before you were going to strip it, maybe because it was too small, you had a lousy drive angle, a rounded over tip, were applying way too much pressure for the size of the fastener, etc., etc., etc. Try to avoid making these mistakes, as soon as you notice you're about to try it anyway. I've caught myself countless times saying to myself, "I'm going to strip this thing". Age has finally taught me to pay attention to this inner voice and stop, rethink and grab a bigger screw.
As to which filler, well you're going to need some silica to control viscosity, but I like to add milled fibers to improve elongation and cross link. Cotton flock (404) or a straight silica joint will do too. I dislike pure silica joints, because you can get dramatically weak areas in it, unless carefully mixed and it's more brittle in compression, which is precisely what a skeg will see in an impact. Both 404 and milled fibers are better in this regard, though you'll still need some silica to thicken it up.