If you can't get MikroC to find your PK3, you can File->Import the .COF file (or .HEX) from MikroC into MPLAB 8.x, set the PIC type to your PIC type and the Programmer to PICkit3.
If the MickroC is anything like the MPLAB interface for the PK3, I have to really baby it to get it to recognize the PK.
If the exact sequence of connecting is not gone through as the instructions say, it won't recognize it, VERY much different to the PK2.
I suspect it is in the driver somehow.
Max.