Well it has to be said, for a PIC-man venturing into the Atmel world there are many pitfalls.
The story so far...
I designed a Jtag/ISP programmer based on the excellent IsoJtagISP. I used Eagle CAD and pcb-gcode to output the design to my little Widgitmaster CNC router.

(Mind the blobs of solder at the top. I bumped the crystal loose and tore the tracks off the board during the many attempts at removing the AVR as detailed below...)
The board engraved a treat and was flawless. Time to drill... oops! I forgot to set the Z height for the "Tool Change" home position, so helpfully the machine engraved a nice straight line across 3 tracks. DAMN! Ok, fix that... drill, drill, drill, DAMN does it again! This time only across one. Repair the tracks with a small piece of magnet wire and start assembly.