First thing you need to buy/borrow a cheapy OBDII scanning tool and find out the DTC. My guess is you have the 'Crankshaft System Variation Not Learned' condition. I had it on my 2004 after my first PCM swap, it was P0315. It may be different for yours, but will be something like P03XX.

Next, you need to find someone with a Genisys (or similar) tool that can perform the crankshaft relearn. It should only take a few minutes at the most if the technician knows what they're doing.

I had several "reputable" auto shops around here wanting to charge me $90 to $95 to perform it. One wanted $110 and told me they needed to charge that much because it was such a "touchy and complicated" procedure. Another said, "Well, that's the going rate". Huh? It's more like they got ya' by the nads and they know it! They will never see me as a customer.

I finally found a local shop that did it for $40 (still to high IMHO). And yes, it took about a two minutes once the tech hooked up the tool.

If you do have the crankshaft relearn condition, it does not hurt to drive it that way for a while. But it doesn't help either. You need to get it fixed sooner than later.

Hope this helps.

Good luck.