This doesn't make any sense when I think about it, and the throttle has always worked fine but it seems as though the throttle cable that goes on the bottom at the throttle bodies goes on top at the throttle tube housing. One cable has to go under the other at one point and that doesn't seem correct. Is this correct? Thanks in advance

 

Better question, does the pull cable go on top or bottom at the throttle bodies?

 

Your TBs only open one way. So if the throttle actuates the TBs, its not backwards.