A little background:
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I bought a Civic 2003 EX 4-door automatic sedan at an auction with 17,000 miles on it. During the next 4 years, I have driven the car here in the New York Metro area and my total is now is 38,000 miles driven. The car never had any of the "suggested" maintanance done on the car except for new tires, new rear-brakes and regular change of oil at an authorized Honda center.

3 Weeks ago, I had the "check engine" light go ON, but 2 days later it dissapeared. A week later I went to do my annual state expection and the car passed. The very next day, the "check engine" light went back ON. I waited for 5 days and then decided to take it to the Honda center for my regular oil change and have the car "check-up".

Maintenance Comments:
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The report they gave me told me the following needs to be done:

Brake Flush ($100)
Front Motor Mount is broken (no estimate)
Passenger Side Motor Mount is broken (no estimate)
Transmission Flush ($100)
Coolant Flush ($100)
Air-filter also needs to be replaced (I can do this myself).

As far the Check Engine Light ON, they would need to do a $100 diagnostic test and even if everything is okay, I would still be charged. I asked them if we can just have the light turned off without the full test, but was told that there is no way to do it without running the $100 test. is this true?

Since I am not an expert, can someone please give their comments/opinions if I really need to do all these above "fixes". The car runs just fine even with the check engine light on. At the same time, I don't want to burn my engine if something is really wrong.

All input is much appreciated!