Can you confirm that you have removed the PIC from the target board, and replaced it with the AC162053, with the PICkit 2 connected via an adapter to the 6P6C modular jack socket on the header? The header should have a 28 pin PIC16F648A-ICD fitted to it.
It may be worth trying MPLAB 8.92 which is likelly to be more stable debugging such an old PIC with a PICkit 2. I have MPLAB 8 set NOT to autoconnect to the PICkit 2 and NOT to reprogram the chip on a successful build, as I have found that when debugging 8 bit PICs, after programming the PIC or header with the debug build it can take a couple of attempts to enter debug mode successfully, and that way, I only have to reset the target from the debugger toolbar (and sometimes reconnect to the PICkit 2 from the same toolbar) for the debugger to start sucessfully. Also, under MPLAB 8, a crashed debugger can often be unjammed by selecting MPLAB SIM then reselecting the debugger, connecting and resetting the target, but on MPLAB X debugger crashes usually require exiting and restarting the IDE, and sometimes need Windows rebooted as well.
MPLAB 8 coexists happily with MPLAB X as long as you don't let them fight over a programmer/debugger or try to build the same project at the same time from both.