Hmm I know there is/was a version floating around on here that supports 240gb HDDs so I'm sure you'll be able to find one.
I'm not sure if version 3.6 will support it but maybe one of the newer dev builds will. Just give it a try, you've got nothing to loose.
You don't need the custom version for 120GB HDD, it will work with regular version just fine.
In order to work with HDDs larger than 2^37 bytes (about 137GB) one should use LBA48 commands, that's why there are custom builds for 240GB HDD.