That’s a problem, and in fact has made it far from easier.
You have reams of JS to trawl through, some pretty dated code, some compressed etc. — needle in a haystack comes to mind.
Checking the official blog, mootools hasn’t been updated in 7 years. Furthermore from what I can see it creates it’s own custom methods on Javascript’s built in types. This is prone to conflicts.
Doing a bit of searching, I have found quite a few old threads reporting conflicts between Jquery and Mootools. The solution being to use Jquery.noConflict() e.g.
Maybe that is relevant.
I’m sorry to say I am with SamA74. You are in need of some modernisation of your code and would probably benefit from trimming down what you have considerably.