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Hello, does the thumping noise happen all of the time or just when going over bumps in the road?
If the sound is coming from the passenger side higher up I would inspect the vacuum pump to make sure the bolts haven't vibrated loose causing it to get knocked around. I would also inspect the vacuum canister and it bolts to the inner fender and can tear itself out causing issues. Once thing to look at are the sway bar links just to be on the safe side. A lot of people over look sway bar links due to not bein sure to tell how they are bad. When you grab onto the sway bar link you shouldn't be able to wiggle at all by hand. If you can they need to be replaced and can cause similar noises to what you are hearing. I would wiggle everything mounted on the passenger side fender and see f anything wiggles. If anything doesn't seem solid It can cause your noise. Once you make sure everything is secure your noise should go away.
This vehicle should have hydroboost braking and not a vacuum diaphragm. The vacuum pump controls automatic 4wd is equipped. The other thing that vacuum pump operates is the vacuum solenoids for the blend door, and recirc door on the inside of the vehicle.