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If you are talking about the weather seals my guess the Honda dealer may be the only source. If its a noise when you open the doors many times its hinge that needs a lubricant oil sprayed on it. Its good to treat the weather seals and window tracks with a sylicone spray lubricate you can buy at any auto parts store.
Many clutch systems are operated by a hydralic master cylinder simular to a brake system. Most use a dOT3 specfication brake fluid same as the brakes. The reservoir is usally located near the brake master cylinder. Look for that reservoir that is smaller that the brake reservor and see if it is low on fluid level. Make sure you use the proper fluid if it needs any. If that does not help your shift issue I suggest you have a professional technician check it asap.
Look for vacume hose that could be split or disconnected. From that point it could be caused by various faulty sensors, wiring problem, or a mechanical problem. Driving with a lean condition for extended period could leed to more problems.
Service professional that has proper diagnostic equipment can look at the computer transmission control system to see if its a faulty signal or a more serious mechanical problem with the transmission. You sould check your fluid level first...that is if the transmission is equipped with a dip stick. If it does not have one a technician can check it by another procedure.
Double check your battery connections. Make sure you did not get the polarity wrong...If that happened the main fuse link could have blown.
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.