Hello Guy,
I'll try to answer your questions below.
1. Pin 1 of the programming port (MCLR) is in the corner of the board, near the breakaway screw hole.
2. To connect to 5V telemetry, I'd suggest using the telemetry pins near the programmer port, plus the spare 5V pin. Like this:
3. I'm not familiar with this GPS. I suggest using the fine-pitched connector labeled GPS, if you have a cable you can use. It's designed for the
EM-506 and its cable. Or you can use the through-hole pins. All GPS pins are labeled here:
4. You're welcome to drill holes in the removable part of the board. It contains no copper, so nothing will block you from wiring it up with your own header, but there's also nothing to solder your own pins onto.
Please let me know if you have any more questions!
Best wishes,
Ben