I uploaded some of my alternative designs here: https://github.com/sanni/cartreader/discussions/311
Maybe they can motivate you a little. 
You need a PIC programmer to program a PIC micro controller but it doesn't have to be the PICkit3.
The ch341a will not work because it's a SPI/I²C eeprom programmer. You can use a PICkit2 or a TL866 or even a DIY PIC flasher for the COM port.
If you can post a picture I can tell you. It's more important to have a supported flash chip like a S29GL### since all the Alteras probably run the same code.