The reset switch it was referring to is the jackpot reset switch on the side of the cabinet, but it really doesn't matter right now. Why were you trying to accomplish by clearing it? It's not normally required.
If you're not using a bill validator there's no need to use a set chip. The set chip is used to enable the bill validator and set the machine denomination. The denomination is only required so the machine knows how many credits to give you for the bill you put in it.
It's not clear to me what you did to the optic wires, but I would connect them the way they should be before trying to bypass them. Post a picture.
Here's a document that may be helpful getting the machine initialized, but you have to repair the optics first.