New Ignition Coils after Check Engine

I recently had my muffler replaced on my 2000 LC, and about a week afterwards, I noticed my check engine light, VSC Off and VSC TRAC lights on while driving. The engine didn't really feel rough at all. The shop pulled the codes and the codes indicated misfires on three cylinders. Even though the mechanic didn't actually see evidence of misfiring, they suggested I replace the coils for those three cylinders. I told them to go ahead and do it. The cost was $479. As soon as I picked the car up from that shop, the check engine light was still on! The guy told me it hadn't been on when it was in the garage, and cleared the codes. Sure enough, later that evening, the lights came on again (check engine always comes on with VSC TRAC and VSC OFF), so I planned to take it back to that shop this morning. When I was driving it to the shop, the check engine light actually started flashing, which I understand is an indication of a hard misfire. Problem is, I just don't feel any misfiring, although maybe I just don't know what that feels like. Even if there was misfiring, the cylinders that are showing misfires on the codes were just replaced! That same shop is looking at it now, but at this point I feel like I deserve a refund. The fact that the light was flashing this morning means to me that the vehicle is actually in worse shape than it was when I brought it to that shop. There are a few things I would appreciate feedback on:
1) Has anyone experienced this type of problem before? - Codes indicating misfires but no other indication of misfiring.
2) Has anyone had to go through the experience of convincing a mechanic that they deserve a refund or partial refund?
3) According to another mechanic, the cause could be a speed sensor (shown in the codes as malfunctioning) indicating a wheel slip and then causing the engine to misfire. Anyone experienced this?

I'm really stuck here. To make matters worse, I'm a college student a bit strapped financially (but I'm still going to pay to fix this one way or another), and the nearest dealer is about a half hour away. If there really is a hard misfire going on, I probably shouldn't be driving a half hour to the dealer. I got a new cat four months ago and don't want to ruin it. Forget about towing.