I can finally report an update.
I was avoiding the repair since I don't have a garage available and the driveway is pretty cold here in Michigan. But I remembered that my brother has a lift in his garage and it is heated. (What a blessing!)
The good news. I was able to replace the flex pipe without breaking any bolts or other frustration. I was also able to get a refund from the repair shop. The new flex pipe resolved the extreme vibration when the transmission was engaged.
The bad news. When the engine idles in park/neutral it is smooth and when the engine has not come up to full operating temperature the car idles pretty smoothly for a four cylinder at about 900 rpm in reverse/drive. However, when the engine gets to full operating temperature the idle drops to around 600-650 rpm and I have a vibration. (It is not as bad as what I was experiencing with the original flex pipe fix.) Still, it is noticeable enough that is is annoying.
FYI, when replacing the flex pipe I did not anticipate needing to remove the exhaust manifold but it was necessary since the upper flex pipe nuts where not accessible without removing the exhaust manifold with the flex pipe as one unit. When removed together, I could replace the flex pipe. As a result, I did not have a new exhaust manifold gasket or new studs which I have read is the proper procedure after removal. I don't know if this could contribute to the idle issue.
While this is an improvement overall, I am still not satisfied with how the car runs currently. Any other suggestions?
Thanks.
Thursday, February 7th, 2019 AT 5:42 PM