2007 Ford Focus Shaking, jolting, and overheating.

P1299 - Cylinder Head Over Temperature Protection Active

Am I to understand you're still trying to drive the car this way??? You're going to turn what might be a simple problem into a destroyed engine. Shaking while the car is not moving suggests the engine is misfiring, and depending on the cause, that can send unburned fuel into the exhaust system where it will overheat and destroy the very expensive catalytic converter. When was the engine last tuned up?

The symptoms you described could be caused by a leaking cylinder head gasket, a failing generator, even nothing more than a bad battery in rare instances. The engine overheating could be a direct result of the problem or a secondary clue, but either way, that is eventually going to lead to a warped cylinder head and a very expensive repair. Your best bet is to stop driving the car immediately and have a mechanic look at. By this time he is going to have a hard time determining which symptoms are related to the initial cause and which ones are results of that cause. You can help by making a list of the symptoms and most importantly, the order they started occurring in.

Yes, I am driving the car. I need it to go to work and school and things like that. Sounds crazy, I know, but I have places to be and it's hard to hitchhike these days.
It hasn't had a tune up. It's a used car and I haven't put much into it aside from the very expensive rebuilt transmission.
It shakes the most when I am parked or when I slow down to a stop. When I'm in motion it either jolts back or struggles to accelerate.

Which is less expensive, buying a different car after yours just won't go anymore, or calling a cab? There is a limit to what you can pound out of a car before it lets you sitting on the side of the road.

Imagine in the wild west a wheel broke on your covered wagon. Then your horse broke a leg. Then the wagon tipped over onto its side. Your lame horse didn't have any food or water for a week. Now you're sitting there whipping the horse trying to get him to take you across the dessert. This is what you're doing to your car. It's not going to get any better. Every mile you keep trying to drive it is going to cost you much more in repairs until you reach the point even a salvage yard won't want it except for the price of scrap metal. If you'd stop and fix the wagon, buy a new horse, and feed him, you'd get across the dessert much faster than by walking!

You may have places to be but no car is going to take this abuse for very long. If you're attending a community college, check if they have an Automotive program. In mine, we were always looking for cars for the students to learn and practice on. The only stipulation is what yours needs has to fit with what we're currently teaching. We wouldn't do electrical repairs, for example, in "Brakes" class. To do so would take potential work away from the businesses in our community that hire our graduates.

Most four-year colleges don't offer practical things but a few do have small shops where they might at least be able to start the diagnosis on your car. If they can make a list of the majority of the problems they find, I can help prioritize them for you and tell you which ones can wait and which ones are critical.

If you're working part-time while attending college, like I did, it tells me you don't have money to waste. If you keep trying to drive this car they way you described it, you're throwing dollars out the window to save a few pennies.