ICSP on an AVR with broken CLKI returns 0x00's
MISO/MOSI/SCK is correct, CLKI is nothing to do with programming/debugging.

Check that the ATmega128RFA1 is supported for your programming technique, otherwise you should buy a Dragon, which offers debugging as well as programming. You will probably need Windows, though.

Posting your schematic might enable us to see the cause of the problem.