I had to go up spacer wise since board is half as thick as the FPE made panel in the original design. I had 10mm spacers there originally but added 1.5mm worth of washers since the button caps were sticking out a lot. You could probably go to 12mm with no issues (I like the buttons sitting low). I am still thinking about what I want to do about the back. Personally, I am not crazy about how it was done on the other case where the core32 was bolted to the bottom panel with standoffs and with the way this case is made, it may be a bit cumbersome. Ideally, I would like just to use L brackets and just mounting to to the panel but I have not really worked out a good way to do that yet with the core (the SD card is easy to do with a standard bracket as well as my 4x I2C board). I would like to do it like TK's case though with the core on one side, DB25/SDCARD/ETH in the middle and the other 4 ports and BLM on the other side.
The panel mounted midi jacks is one thing I am considering along with a panel mounted USB port as well which would solve the board mounting issue.
As far as the LEDS go, I had no problem just hitting both leads and adjusting the height after I had soldered them in initially when I was trying to decide if I wanted them flush with the top of the panel or sticking out but that probably wont work for the 3 prong ones.. You could always just put standoffs on the board and flip it upside down, lay it on something flat, and solder them in like that, no guarantee that they will be perpendicular to the board, but the height should be the same that way