Regardless of whether the shop should have plugged the holes prior to painting, I found myself in a situation where cleaning the threads was needed.
I set about to remedy this by getting a proper sized bolt, a vice and my 4 inch angle grinder.
So first step is to find the proper bolt for your threaded hole.
Step 1: Prepare to Grind
Start out by making a tapered grind along the length of the bolt on the threads. The taper should be a fatter/wider grind at the bottom of the threads and thinner at the top.
Step 2: Attention to Detail
What this kind of cut will do is allow you to easily start the bolt into the threaded hole. As your bolt progresses into the opening debris will collect and fall away from the 90 degree cut and into the hole via the ground down opening in the 11 o'clock position. The further you put this chaser into the threaded hole the more clean the threaded hole will get, since the taper of the bolt grows smaller and allow less tolerance between the threads.
Now, I know some people would suggest just using a tap from a tap and die set. But taps are meant to cut metal. We're only looking to remove, debris whether it's paint, dirt, or rust and other corrosion. The tap could actually shave your threads in the hole making them thinner, which would allow for slop in the bolt or make the threads weaker, depending on how fine or course the thread set is.
Once you're done with this throw it in your tool box. You might be surprise to see how often you might need it.