There is a clean out on the rack with a filtering screen that should be removed and cleaned. Search this forum, There is much discussion about this . The clean out has a large Hex head ( If I remember correctly )
The calipers hold the pads, The pins guide the calipers from standing to compression and back to standing, There are no holes in the pads that the pins go through.
The bolt is not going to get better by itself, The sooner you replace the better, What happens next time ? What else does it effect ? Change it out !!!
Make sure the hex wrench fits the bolts tightly, Insert the hex wrench and tap a few times with a light hammer, Then turn them. They will come out, You take the chance of stripping the hex more that breaking them off.
I had a 98 GS300 FOR 225000 Miles, I went through 3 Master/ABS cylinders, I think there is a subject on using a brake booster from a SC430 Check into that.