Rough idle and shaking, sputtering, dying when turned on

It began overheating and leaking coolant so with deductive reasoning, we figured the water pump had failed. Because it is our only vehicle and we still had children to get to and from school, and a husband who needed to get to work, we had no choice but to drive on it and just fill the radiator with water multiple times a day. After about a week, we had the time and money to replace the water pump and thermostat. We did that and as soon as we added coolant and turned the vehicle on, white smoke poured out of the exhaust pipe, the check engine light was blinking and we got a cylinder 3 misfire code. We then had the head gaskets replaced and while the code is cleared (odometer reads done) and there is no check engine light, there is still excessive shaking and a rough idle. We're admittedly 8k miles overdue for an oil change and our mechanic said the oil was a bad color so that's being changed today. He also said he would re-tighten all of the bolts. Aside from that, what else could be wrong?