in regards to the stiff HDMI cable:
recently ran into a similar problem when modding a laptop mobo into the back of my TV. Those cables can be unruly. one thing you can try is small polyethelyne (sp?) 90 degree tubing elbows. just take that dremel of yours and cut a slit on the inside of the elbow, running from opening to opening so that you can pry it open some. stuff the cable in, and it holds a tight 90 degree turn in it. might eventually cause some stress on the wires, being that its so close to the connector, but could be worth a shot. you can find these elbows at lowes, home depot, ace hardware, or any plumbing or air conditioning supply house.
to the guy who posted that SD extender ribbon from a few posts up: THANK YOU! that's gonna solve a problem i have with a project of my own.
a few suggestions for the project as a whole: the decal would look great on the front, on the cart lid. Id put it to the far right, to offset the NES regalia, and justify the text to the right side instead of the left. also, im not sure how much of the original case look your trying to retain, but the usb port would probably serve more purpose on the front of the case (and any sd card extension you may choose to install).
youve undoubtedly heard of websites like benheck.com, but if not, youd do well to check out the forums over there for any fabrication tips, techniques, etc. no, im not affiliated with them, just thought id help
anyways, good luck! its an interesting build.