I've done this conversion once. It was the most labor intensive project that I've attempted. I went the top mount route, instead of the recessed mount for pure aesthetic reasons. I personally feel the recessed routes are ugly.
The pass through area on my guitar needed to be filed a bit, not actually re-routed or anything. I just had a small spot that was rubbing the underside of the arm assembly. Of course YMMV. I also had to buy a 42mm block instead of the stock 37mm block didn't quite clear the route. When I depressed the bar fully my springs would catch in the route.
I didn't fill the holes. The issue I had was that the guitar was a swimming pool route, and the studs were too close to it. They eventually began breaking into the pickup cavity, so I had to dowel, redrill, and epoxy the hell out of everything. Of course, I was stringing 12-52 standard, so that might have had something to do with it.
Another thing to consider is shimming the neck. Not necessarily difficult, just an absolute pain to shim, adjust bridge height, detune, take the neck off, re-shim... 3-10 times.
Also, depending on the tools you have available, you'll have to decide how to go about creating a shelf for the locking nut. Every how-to that I watched showed someone using a router. I wasn't all that comfortable going that route though, so I used a straight file and took my time.
In the end, everything turned out great. I've since parted that guitar out to build a new one, but it stayed in tune like it never had before. Since then I've decided that if it doesn't have a Floyd then I'm not interested.