Hi SalesMan,
I do believe I know what the issue is you are experiencing after the Sync Engine Update, this shouldn't have anything to do with your "mistake #1". When you perform the update, you need to have QuickBooks generate a new "Method Sync Engine" Certificate. The only way this Certificate will get generated by QuickBooks, is if you are logged in as the Main QuickBooks Admin User. If you are logged in as any other QuickBooks User, you do not have the correct permissions and wouldn't be able to generate this Certificate.
I have a feeling all you would have to do is completely close down QuickBooks to be safe. Then, reopen it, login as the main Admin User, if the certificate still hasn't popped up, then locate the Method Sync Engine and login to this, at this point you should definitely see the new Certificate.
We actually have a blog post with some screenshots here, you might also find this helpful.
Please give this a try and let us know if this fixed your sync issues. If you are still experiencing issues, it might be a good idea to give us a call here in Support and we can troubleshoot this with you. You can reach us at 1-888-925-6238x2.
-Ben