I recently acquired a set of Shimano 560 cantilever brakes for my trek 8700, the mounting bolts for the rear are too long (front is fine). I am also in need of the cable guides for the front and rear. I have searched and am coming up a little lost. If someone could direct me to the parts I need to make this work that would be great. Thank you

Most (but maybe not all) canti studs have M6 internal threads. You can use any high quality screw you want, or just put a couple of washers on the outside to use fractionally longer screws you have.

Cable guides?? Do you mean straddle cable and saddle:
https://www.amazon.com/dp/B001CK0F0W...=IHKA3LF9CB68C

or hangers?
https://www.amazon.com/Tektro-Front-...B4EMKJ3Q5JVK1E
https://www.amazon.com/Origin8-Seat-...7JV60V5DSYR2BM
https://www.amazon.com/Tektro-Hangar...B4EMKJ3Q5JVK1E

The mounting bolts are not specific to the brakes, any pair will do.

What do you mean by "cable guides"?

I would suggest a fork crown mounted cable stop/hanger like this one: https://www.amazon.com/Tektro-Front-.../dp/B006GHDRYC it will help avoid brake shudder: Technical Q&A with Lennard Zinn: How to stop cyclocross brake chatter | VeloNews.com

For the rear, here are two examples: https://www.rivbike.com/collections/...nt=23334913473

Mounting bolts can be cut down with a Dremel tool with a cutoff wheel, or an angle grinder, or just buy the right length at the hardware store. Don't tighten them excessively tight, you can mushroom out the end of the stud and cause binding.