No doubt there, that's a general risk for any kind of DIY.
I've personally found that drilling aluminum cases isn't too terribly hard, though, especially simple circles. I just use a regular hand-held drill and standard drill bits. I first cover the aluminum with masking tape. This prevents scuffs and scratches during drilling, and also gives me something to draw on. I draw and annotate all the cuts I intend to make. Measure thrice, cut (or drill) once! I just clamp the aluminum to a piece of scrap wood so the aluminum doesn't bend while I'm drilling it. Then I use a deburring tool (
here's an example) to clean up and smooth over the rough edges of any cuts. This results in pretty decent holes, and any remaining imperfections get covered up by whatever goes in the hole anyway.
As you get over 1/2" or so in size, drill bits get expensive. So, for XLR hole cutouts, I spent the money on a punch. I build enough audio electronics that it's paid for itself.
If you want to machine non-circles, it does get trickier. For me, the only non-circle I need is the IEC cutout. What I've found is that the cheap Chinese chasiss almost always come with the IEC cutout. Also, if the aluminum is thin enough, you can use a cheap handheld nibbler tool to make non-circular cutous. However, if I'm going for something a bit nicer, I'll spend the cash to have it machined professionally (e.g. diyAudio store, Front Panel Express). But I've also gone without an IEC completely, and just had the power cable permanently attached, going through the chassis via simple circular cutout with a grommet (and an internal cable clamp).
If you have zero chassis-working experience, you probably don't want to make your first attempt at metalwork on something as nice as the Mod-686. In that case, either pay for someone to do it for you, or first spend some time practicing on cheaper builds.
Oh, there is yet another way to really save on the chassis: hit up thrift shops on a regular basis, and wait for some cheap/old used components that have an appropriate chassis you can re-use. I see people on diyAudio doing this fairly often. If you have the heatsinks, you could even use something like an old PC chassis!