I've prototyped the PicKit 3 clone before doing a full layout. I built a breakout board for the PIC24 QFP in KiCAD then added the surrounding circuitry on a breadboard. Right now I don't have the VPP generation or the level shifting buffers as I wanted to prove to myself that I could program a 3.3 volt device before I had board built.
Using the firmware image above (and a few others I found off the web), I can successfully load the bootloader, RS, and AP for PIC18s through MPLAB, but I get an error of "PK3Err0026: Download program exec failed." when trying to do the same for PIC24 or PIC32. In all cases the firmware RS and AP loads initially seem to work OK before giving the error when the PK3 tries to re-connect after reporting a successful update. I can read the VDD voltage correctly in MPLAB even after the error occurs. I'm not sure if my problems are due to a bootloader hex that is not valid, taking too many shortcuts on my prototype, or just that the PK3 firmware is flaky even in production devices.
I too would be interested in what SPI memory is mounted on the PicKit 3. Does anyone have one that they can look at? I currently have the SST25VF040B on order but have not used it yet. I'm using the 25X40BV from Winbond right now as I had it already - that may be part of my problem.
I hope to prototype the VPP generation shortly as well as hook up a logic analyzer to the SPI memories to see if the PK3 is trying to read/write those. If anyone has made more progress on a clone, I'd be interested if they had any similar problems.