I’m considering ordering a second keyboard, but since I use a custom layout I’d like to have it with basically the US layout except with ISO enter and both left and right shifts split, i.e., 1U \| key between left shift and Z, and Fn key next to right shift. Is this possible, and what layout options should I choose? Also, is it possible to order a Ctrl key that fits in the caps lock position?
Yes this is possible – just configure the keyboard with the regular US key set and please see the previously answered question here for details on what else needs to be ordered for the customization: https://www.modelfkeyboards.com/questions/question/iso-layout-with-hhkb-for-mac-and-extras/
For your Ctrl question, yes, the HHKB layout will include the swapped Ctrl keys, among other keys noted here: https://www.modelfkeyboards.com/product/front-printed-keys-f1-etc/