2000 Mercury Cougar Intake gasket

The car was free from a family member. It sat for about 2 years, after they were told that it needed a really thorough tune up. It was not in a wreck. There is hardly any rust on or in the car. I am looking to get it running to save gas commuting to work. I have checked all of the spark plugs, vacuumed out the mice nests under the hood, performed a spark test, and diagnosed an intake leak. I did a compression test before I found the bent flap. I have been working with a family member who is a mechanic. However, due to the fact that this engine sits sideways and neither of us have dealt with that before, we are at a stand still. He told me that without compression, the problem could be a lifter or a hole in the piston. That was before he knew about the bent flap. The car starts and has driven down the road. It backfired because of the vacuum leaks. Now I have the top side of the motor apart, down to the intake gaskets. Do you think this car would likely run with changed gaskets and reattaching the control arm? I have found the square clips that the control arm goes in to. The clip was missing when I got the car.

I think I did not communicate it correctly. I was talking about the throttle control arms that control the flaps on the intake. If this changes any of your advice, please let me know. Otherwise, I will check the things you suggested. Thank you for your time and information! It is greatly appreciated.