I am absolutely anal when it comes to cable management so I think I can give you a few tips.
I don't know what kind of cash flow you have. But if you can afford it, I
HIGHLY suggest buying a stepped drill bit.

For cable management you'll need ~ 1 inch or so. They'll run you about $60. But over the years I have spent twice if not three times that much on cutting wheels for a dremel. You'll also need a good 1/2 chuck drill to power it.
Cut the holes under the motherboard tray and make sure that they won't be seeing once the motherboard is in as IMO it wrecks the image. Buy some grommets for the holes after they are cut. You can get them uber cheap at Performance-PC's or you can buy them at home depot for a tad bit more.
As for painting. If you want it done right, take it apart. Don't be afraid of rivets. They are actually fun to replace. You'll need a rivet gun which is ~ $20 or so @ CT. And rivets are dirt cheap. Steel does not need to be primered as it isn't porous. Some people say it will make paint stick better, but really it won't improve anything. However make sure you clean the hell out of the metal with soap and water. Oil/dirt on the surface will make things very nasty. If you are going with a flat colour, there is no need to sand between coats as long as you don't have any runs. After the last coat, try to let it set for a good 48 or more if you can afford before putting it back together as it will chip quite easily early in its life. Also go for enamel paint.