I've used a hole saw as well. My only suggestion would be to remove the panel and put it on a piece of wood for support and reduce burring. Use a hole saw with a high teeth per inch and take your time.
This is one of the reasons I went with the Styx over the Metis. Other reasons being the option to go with an mATX board next time I upgrade and the optical drive. And I got it for a really good price from a fellow OCN'er
Since it's aluminum forcing a larger screw might work, but it won't be a very clean job and I'd worry about it stripping out again. Ideally you'd need to go to your local hardware store and buy an M4 tap and tap handle. Once you have though retapping the holes shouldn't take more than 5-10 minutes.
Sounds a lot like my build, except I used a Styx instead of the Metis. I have a Silverstone Strider Platinum 550, which is 140mm, and a full sized 980ti and there is no fit issues. I also have the Ereboss Core Edition cooler in there as well. I've been thinking of switching to the Metis though, so you'll have so make sure you post pics when you're done