For the longest time, I had a "thunk" sound when I started the AC in my truck. It's not consistent, but it does happen and it also marks a loss of AC performance in general when it does.

Second, when the AC DOES work, I get a musty/mushy smell in the truck. I've vacuumed out the roof vents, and I'm looking at one of those AC cleaning spray kits for when the air is decent again.

Suggestions on what to fix/replace for both?

 

The thunk could be something simple like loose bolts on the compressor. Try having someone turn it on while you have the hood up and are watching the a/c assembly. As for the smell, has anyone smoked in the truck? Smoke particles settle in the ducts and grow mold. A cheap and quick fix, but it doesn't last forever, is to open ALL the doors and windows. With the fan blowing on high, spray Lysol disinfectant into the air intake grill at the base of the windshield. This will clear it up for a couple of months. In the winter, the heater will keep it dry, but some next summer, the moisture will let it grow again. BG Industries used to sell some stuff call Frigiclean, I think. It's a foam you carefully drill a tiny hole in the duct housing and fill it with a cleaning foam. Let it sit for a while and it will generally take all the crud off the fins inside. If a previous owner has a HEAVY smoker, figure on a new headliner down the road as it tears the foam up just like your lungs.

Lysol though is cheap and easy.

 

Your AC compressor clutch may be going bad. They all have a slight thunk when engaging but shouldn't be something you notice. The clutch alone can be replaced without pulling the line$, but it does take a bit of patience. There are youtube videos showing the process. I replaced mine with a junkyard clutch when the idler bearings went bad.

 

I have one of these little gadgets. Bought it shortly after I bought my work beater, because while I knew it had been smoked in I didn't realize how bad it was. The car dealer had some pretty good masking spray for it, but after a week the inside of the truck was unbearable. It was as though a pack of wet sheepdogs lived in the truck, and every last one of them was a carton a day dog. Horrible. I even took it to a professional who did a full steam-clean on it, no effect. The ozone generator, on the other hand, was extremely effective. It did take several hours of runtime, but the first dose knocked the smell down to a tolerable level, second run knocked it down further to acceptable, and a third run made it so my wife (who is asthmatic) is now able to ride in the truck.

It'll leave a strong chlorine smell in the truck (think indoor swimming pool) for a few days so you'll want to give it a good airing, and you don't want to get a deep breath of this stuff in. After you run it, leave the doors open for a few hours. If you want to clean the HVAC out with it, then put a battery charger on and leave the blower motor on high while the ozone generator is running and have the generator pointed at the blower inlet.

On the clutch, if the clutch is worn so are the compressor innards. If money is tight, replacing it will buy some time to save for a new one, but if the innards let loose it'll contaminate the entire system and all parts in the system will have to be replaced. Not replacing everything with a blown compressor means the new compressor will blow shortly after it's replaced. Replace only with a new one as well, a reman is rebuilt to much looser standards than a new one, if at all. In many cases it gets shipped to a third world nation where they dip it in cleaner that isn't allowed in the US (in other words, stuff that works) then it gets painted and sent back without ever being cracked open.