Welcome to the forum for starters. Sounds like you have a lot of little items that do need to be taken care of, do them one at a time. Broken bolts are always fun and a pain, it isn't just a Mopar thing, it is all brands, water ones don't help, usually neglect in using just water makes it even worse. So, start with the broken bolts first, removing the water pump and thermostat hose, soak in solvent, then work on drilling them out, helicoil as necessary if it comes down to it, they aren't going to fix themselves or not leak otherwise. Cleaning the wiring for the transmission is a matter of pulling the wiring loose from the connector, a lot of them have some kind of a clip that is very tight that has to be undone, like a red plastic piece that unsnaps or a button that has to be pushed to get them to unlock, pull the tape off and clean, myself, I prefer something like laquer thinner. Let them dry, rewrap with, I prefer, 3m cloth tape (I get it from electronics stores), feels sticky, but stays together and doesn't come apart in oil like black electrical tape does. Stop the trans pan the same way as the others with either oversize bolt and a retap of the case to match, then drill the oil pan hole out to match. The banana shaped thing is a purge valve, takes vacuum when engine reaches temperature and helps maintain burn temperatures in the cylinders and sensor operation, computer controlled, funky, but, get a vacuum diagram, check the condition of the hoses, replace if loose or hard when squeezed, they are probably leaking at the connections if not cracked, so vacuum signal isn't operating properly, the clicking indicates they aren't able to route the vacuum properly and it is cycling to try to fix itself, which it can't with bad vacuum leaks, which may explain the smoking, too.