I used the dumb way shown in youtube to check the coil packs, and apparently none of them are completely dead, for as soon as I disconnect any, the engine vibrate more.
But the shop said 4 coil packs are bad and better to replace all six. He has Hitachi pack which is $75 each.
So total bill $75*6*1.09+125, total a bit over 600. Drove 20 miles after pick the car, seem to be smoother than before the misfire happens.
The car probably worth 3-4k now. Spending 600 is significant but I can still take it. The car has another problem, losing coolant slowly. Not repairing now, may try some gasket repair liquid later. Good for a few years as long as I add coolant every other week for commute.
My former coworker has an old sienna van, got hit, and insurance company refuse to repair and gave him a few thousands. He complains he can't find used van as good as that one for the money. But he bought an Infiniti afterwards :-)
Thanks everyone for your help. Could have been overcharged a bit, but not too bad...