Hi Andrew,
Whether it's the filter being clogged or the pump failing, that would lead to the mixture being very lean so that would produce a lot of extra heat, hence the glowing pipes. I would say that getting the pipes to glow with just a short spell of idling does not sound good to me and needs sorted out. If everything is basically working correctly then going from standard to the Stage 1 pipes and filter does cut a lot of the heat so everything runs better but if the fuel supply is compromised then who knows what happens.
The S&S specialist is Matts Machine Shop, the website isn't really up and running but has a phone number and email address.
I think there is a port on the high pressure part of the fuel lines at the throttle body but don't know for sure; haven't had to check mine!
There has been at least one thread about which pump fits but I haven't been able to find it - have a feeling it may be one from an X5 but really not sure - hopefully someone will be along soon who has done the job.
Best of luck getting it sorted out.