Quoted from aobrien5:
Make sure the left or right gate isn't getting in the way of the beam. Hold the left gate open when you're doing this. Perhaps your pounding the playfield is enough to make the left gate bounce out of the way.
I want to thank you guys for your help, aObrien5, kporter, and phishrace, you guys rule. After inspecting the gates some more I noticed when I would give the SLIGHTEST of nudges to the left gate the switch would read closed again, i did this a few times, opened the switch, it would stay open, and then basically the smallest of movements from the left gate would cause the switch to close again.
I noticed if i held the gate over to the side a bit, the beam would open and close no problem, so for now, I put 2 flat washers around the gate wire to keep it to the side.
I guess Im hoping this is the only issue, in all the threads I read i never heard of the gates being on issue for the long opto, but i played a few games on it, and all of the symptoms I have mentioned seem to have gone away. We shall see though. I will be making all of those checks you guys suggested though just in case.