serial port program - many. I like Bray’s terminal
Google brays terminal. One place
http://braypp.googlepages.com/terminal
MISO, MOSI, SCK are logic level signals. If you are seeing +/- 12V swings, either your scope is grounded wrong or some such, or there’s a big error in the circuitry like the zener diodes are missing, backwards, or some such.
It’s really worth the $30 or so to have a real Atmel ISP - these days they’re USB, not RS232.
The one your’ building tries to big-bank the logic levels via serial port toggles.