Yes, it was very painful at first. The things that offset the pain is that at the start, the code was strictly the same (C code) for x86-64 and 6502, so I could iterate bugs out with the x86-64 decoder before trying with the 6502 code, in a few milliseconds. Afterwards, once I started going assembly on the 6502 code I iterated over that using MAME's Apple IIgs with 16MHz ZipChip, making the wait ~5 minutes instead of 70 at start, and less and less as I progressed.

Thanks :) I do time the 6502 code using the MAME emulator, its debugger's trace feature, and a profiler I made. It's far from perfect (gets very confused by tricks like pha/pha/rts in the IIe ROM) but works under IIc emulation and allows me to precisely count cycles in my code: https://www.colino.net/wordpress/en/a2trace-debug-and-profil.../