I wanted to close this thread out so that if it is searched in the future, the people have answers. You're welcome future peoples... I got the truck back last week and all is well. Luckily, the mechanic was correct that a loud injector was my issue. The truck also had some much needed maintenance including valves checked, valve cover gaskets + cracked VC replaced, Timing belt, Water pump, vacuum hoses replaced, fuel filter replaced, fuel line replaced, injectors replaced, and Front + Rear end links replaced.
I think my mechanic also did me a few favors including bending my running board back into place so that my slightly taller tires don't rub when turning left at 3/4 lock. He also found me a used fuel door because the hinges were bent on mine causing it to not open completely. My wallet is lighter but the truck feels much better and now I actually trust it on road trips. For the peace of mind, completely worth it.
Thank you all for the suggestions. I'll also give a shout out to Ben at Daisy Import Auto (Woodbine, MD) in case anyone in Maryland is looking for a good shop.
As the S2000 takes a sigh of relief and re-enters hibernation mode