rough running

I have a 2011 Prius that is giving me fits! a while ago it began running rough at startup for a few seconds. The engine will shake and rattle and then smooth out and run fine. I have had it to a local shop for some repairs and they checked into the problem. Had codes PO300, 01, and 02. They checked the plug and coil for cyl #1 and also noticed the coolant level was low. They filled it up and a week later the CE light was on again along with the rough running and coolant low again. They suspected a head gasket leak but said they could not tackle the job. I took it to a Toyota Dealership who checked it out according to the history I gave. They said they could not find evidence of a head gasket, coolant leakage problem. They pressure tested the coolant system overnight and said they could find no leakage. I suggested they put a scope in each cylinder as they had the plugs out anyway. They said they did.They put new plugs in it (the others were only 30,000 miles old) and said they thought they fixed the issue. We had the car for two days and it all started over again. Now I have an appointment to take it back again nest week. I mentioned to them the TSB"s about a timing gear and intake manifold causing similar issues but they said they checked into this. The car has 180,000 miles on it and otherwise is a great car. I bought it 30,000 miles ago and it has been running fine until lately.I just want it fixed and need help. Any ideas?