The mechanic had it in the shop for 4 days?? These Toyota guys or general mechanics? With a Toyota handheld diagnostic scanner (pulls codes, freeze frame data, puts the ECM into test mode, etc.) - they could rule out quite a few things in a matter of hours.
As for what it could be, could be any number of things - what else did the shop do? Did they even do the basics, i.e. check for fuel and fire?
Did they check compression?
Did they test for adequate fuel to the affected cylinder?
Check the injector?
Check power to coil pack?
What did the old plugs show - were they wet with gas, oil, completely dry?
How old were the original plugs?
How many miles on the car?
Good maintenance history?
Did they test the gasoline?
Did they try and pump in some fresh gas?
Checked induction system (air filter, air box, MAF sensor, etc.)?
I could go on...
How did they mechanic determine that coil was truely bad? Did he check for spark? Did he check for power? I hope you are keeping all the original parts - as this looks like it will be a parts swapping type of experience, blinding replacing parts until you hit upon the culprit. This sounds like it could be an expensive fix for a potentially simple problem.