[wiswind]

When you disconnect the battery for more than a short time (a few minutes) you lose some of the stored information.
Getting more to the point......you have "reset" the system....much as you do by pressing the "clear system" aka "reset" on your scanner..
All of the tests have to run and PASS in order for the system to give you a "ready" indication.
The "Ready" indication is required in order to pass emission testing in many states.
This prevents a person from doing a "reset" right before the have the test done.

The system that is usually last to complete the test is the downstream oxygen sensors......"catalyst monitor".
I put a Walker "direct fit" catalytic converter pair on my '96 windstar. It would take up to 1 month of normal driving for the catalyst test to complete.
I am guessing that the aftermarket converters were not a efficient as the OEM ones.

The other issue that you have is that it may have old gasoline in the system.
You might give it a treatment of Berryman's B-12 Chemtool and run that tank of fuel through the system.
Then change the fuel filter, if it has not been changed lately.
The biggest improvement will be running through the old fuel and getting onto new fuel.
Also, make sure that you are up to date on your routine maintenance items.

The battery that was dead.......if you are still using it......it may need replacement.
A weak battery can also cause lots of strange problems.
I figure that 5 years is what one should expect out of a battery, many last much longer, but you should be able to count on 5 years.
However, once it has gone dead, the expected life is much shorter.
The cost of a new battery is low compared to the inconvenience caused by it going dead and leaving you stranded.......or having you going in circles trying to track down the strange problems that a weak battery can cause.

It is not unusual for a vehicle that has been sitting to give you strange problems for a while once you start to use it again.
Some of those problems may clear up on their own after a few weeks of regular use.