How much does a 60,000 mile tune up cost for a 2004 Mach 1?

As far as a tune up is concerned, changing the plugs and fuel filter along with the oil is about all that happens. As easy as changing plugs in a 2V is, a 4V is even easier. The check engine light is probably a O2 sensor.

A dealership will charge a lot more than its worth for the tune up. Except for disconnecting the fuel filter, there is nothing to a tune up that can't be done with hand tools in your driveway. There is a special disconnect tool that costs about $12 at the local parts store for the fuel filter. Let us know if we can help.

Yes Autozone will check codes. I think almost any autoparts store would do it. In addition, a budget code reader cost less than $80 at Sears.

The flashing check engine light means that a misfire is occuring. Suspect an ignition or spark plug problem.

Prob a bad cop or fouled plug easy fix.

Plugs are easy on the DOHC (even easier than the SOHC). Remove the coil cover, pull the COP off, and remove the plug. You'll need socket extensions as the plug wells are deep, but chging plugs on these mod motors is much easier than with the older cam in block motors. Since these are aluminum heads, you should dab a bit of anti-seize on the threads of each plug. (Pick this up at any auto parts store). Also of note - the DOHC COPs are not held in by a 7mm bolt like the SOHC COPs are. Finally, you should blow out the plug well with compressed air (buy a can of it if you don't have a compressor) after removing the COP and before removing the plug. And DO NOT overtighten the plugs. There have been many debates about using a torque wrench for these, but I (and many others) have never had an issue with turning it finger tight then cinching it down with a little twist, using minimal force.
The Mach 1 engine has COPs - Coil On Plug technology - a single coil for each plug. There is no distributor, no plug wires...it's very basic. It uses 8 spark plugs.
Chging the fuel filter is very easy as well. As mentioned above, you do need a special tool, but it's pretty inexpensive. The first time you chg it, it will take you probably an hour...the 2nd time, it'll be more like 10-15 mins.
You should really consider doing these basic maintenance tasks yourself - save money and learn a little about your hot rod. A good resource for the fuel filter change (and the plug change, although this webpage deals with a SOHC...just realize that you have to remove your COP covers (2 small bolts) to gain access to the COPs) is BULLITT Archive Home Page - Many of us out here on StangNet have used this excellent resource.
Best of Luck!

If they said they couldn't check the codes because the light wasn't on, then they were blowing smoke. Any code reader can check code history. The computer archives all codes until they are erased. If they did that to me, that store would have received a complaint on that individual at the very least. At worst, they would have permanently lost my business. Just my two cents.