what do i do with the bolts from the outer chain guides?

If you got new bolts use it-don't use the old ones-that's if I understood you correctly

i mean after i eliminate the two guides do i leave the bolts in or leave them out?

If they go all the way through and seve a purpose, put them back in. If all they did is hold the guides, don't worry about them.
PS: in the future, make your responses to your original question so the whole story stays together. Nobody but me had any idea what the history here was.