Is there a good way to do this? Special rod, or bore guide? Also it seems like my saddle always gets pushed down rendering it useless, anyway to keep it in place? I don't want to go any harder than thumb tight on the knobs.
for a proper cleaning with a rod you'll have to remove the saddle. and to tighten it up you can get 2 headless hex set screws and screw them in on the opposite side of the factory thumb knobs, that way you'll get 4 points of contact on the tongue of the saddle.
I have the same issue on my SPR. I just remove it everytime. Something you can do to stop it from slipping down is cut a piece of wood, or plastic, or something down in the hole that will keep the cheek rest at the proper height without falling. The key is to make the piece fit loose enough that you can pull it out if you need to adjust it's thickness to adjust your height