T2 high byte is not supposed to work in the free running mode. I hoped there is some hack to make it work, but considering not so precise emulation and lack of real hardware (not even sole 6522 chip) on my end, I can't do tests. Well, the main issue with pushing PET is that it isn't emulated well (not all timer modes covered, for one), and there is like 1.5 PET emulators around (.5 in MAME, difficult to setup).
To me it seem the only viable way at the moment is to use IRQ to toggle CB2, I did it as a software Shift Register imitation there. However, there is some issue on the real HW that is not figured out yet is that some tones disappear when you switching between IRQ and Shift Register (just on the transition point, maybe IRQs get skipped?), and this behavior is not emulated (works just fine in emulator).
Another issues are that default IRQ handler pushes all the registers before going IRQ trampoline, which wastes a ton of time; default system handler still need to be called once a frame (to make keyboard input work for the game), which introduces clicks; and unexpectedly annoying one, speaker in PET barely can reproduce low frequencies, they're getting very quiet.