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Replacing a computer should only have be done in few cases. It should has to be done by a trained technician and only after all proper diagnostics have been done first. Without a proper diagnosis many parts are replaced unnessasrly.
At the top of this web site there is a estimate button. You can fill in the blanks of year, make, model, etc. put in the repair you need and get a general idea of the high and lows of a paticular repair in the area where you live. Note: No such thing as a cheap headgasket repair.
I cannot say they caused your problems or not...since its been 5 months and axle seal is not near the work you list I think its not likely. If you feel uncomfotable with that shop I suggest you get recommendation from friends, coworkers, etc. and take it to another shop for a second opinion. If they tell you need same repairs for simular cost you will know about the estimate part. You can ask that shop if they think someone doing the pervious service could have cause these issues.
When the check engine light flashes that means the on board computer is detecting a misfire. That is very important that it be taken in and fixed asap. Continued driving with a misfire can damage catalytic converters. If this work is it its warranty period ....the shop that installed the engine (in my opinion) should be correcting the missfire condition. I highly suspect that is what you discribe as shaking.
Its sold as an assembly in most cases. Aftermarket manufactures may have it also but sill kinda pricey. Check with the muffler shops or exhaust specilist in your area. Some can get a universal replacement flex section and do a cut and weld. That optiobn will be less cost.
Its going somewhere....worse case its a bad head gasket and engine is pushing it out the tail pipe. Could be a slow leak you may not see. A cooling system pressure test is needed to check for external leaks first.
If the " security" lamp is not on in the dash cluster it could be the ignition switch, starter motor, or still weak battery or poor cable connection at battery. Next step a technican would do is check for a voltage signal on smaller wire at starter solinoid when ignition is in the crank position.
Not to give a smart alect answer but its out of gas when it stops running....Not a good practice to run fuel tank near empty often. More chance that the fuel pump will draw sediments from bottom of tank and not good for wear and tear on a elecric fuel pump. Also the fuel in the tank helps cool the pump. I guess the orange means "caution" tank is near empty...time to refill.
Did you take car in for a alignment issue? Or was it in a shop for rotine service and it was "oh by the way we noticed something else." A small dry crack in a bushing in itself is probaly normal for the age of the car. Unless you have a tire wear issue or pulls one way or the other when driving on the road I suspect the guys that said it was ok is correct.
Its located on the evaporative emission (EVAP) canister (near fuel tank)