Transport sync and triggering are two different things, there seems to be some confusion in this thread?
If you want to trigger the TR-8 from Pyramid then probably best to turn off transport sync, I believe you would just set the clock source to internal, but I don’t own a TR-8.
If you want to sync the transport of the TR-8 to Pyramid then best not to also send note triggers and CC data.
Personally I’d choose to trigger the TR-8 from Pyramid as it offers much more sequencing power than the internal TR-8 sequencer, so I’d turn off transport sync on the TR-8, and also on the Pyramid port if no other devices on that port need it.
As mentioned by others midi is a serial protocol, so a bit of planning and consideration of setup is required for best performance. Try to spread your gear across the 3 physical outputs as best as possible, I have thru boxes connected to each output, and do not send midi clock from Pyramid most of the time on all 3 physical ports.
Midi clock takes priority over notes, so if it isn’t needed turn it off.