Car misses and shuts off at times.

[DANWV]

My 98 beetle has an issue where it will all of a sudden start missing and bucking and carrying on until it dies.
It is a 2.0 auto.
I had to pull engine to replace the front trans seal. It did not do this until I put the engine back in and ran it for about 2 weeks after. One day it just took a fit while driving. Got it home and checked the sensors accordingly to my bentley and them seemed fine.

Did not have a scanner at the time.

It sat for about a week until I could get back to it. I read somewhere to pull battery cables off the bat. and touch them together for about 30 seconds. I did this under the impression it would help nothing. Hooked everything back up and started the car. It ran fine for about a week and then it did it again.
Bought a Max-Scan 405 scanner.
I got the scanner and hooked it to the car.
The only code present was a code for the purge flow or something I think it was 0411. That would make sense since the secondary air pump is not currently on the car.
Not seeing any other codes I again pulled the battery terminals off and touched them together and replaced.
Started it up and it runs fine. What am I resetting by unhooking the battery and touching the leads together.
Why is there no codes present when the car is throwing a fit to where it won't even run?

I have replaced:
timing belt
tensioner
h2o pump
a couple vac hoses
plugs
wires
coils
coolant temp sensor
fan switch
This car is driving me crazy.
Any ideas?

[pencilneck]

What are the fuel trim readings after the car has been running for a while?

[DANWV]

pencilneck,
I am not sure on the fuel trims. I don't think I can check those with the scanner I bought, can I?
Do I need someone with VAG-COM diagnostics to see those?
I don't think there is anyone close to me that has that software.
The car runs fine and just like someone flips a switch, the car throws a fit.

[2005Beetle]

...I assume. With no temperature gauge, who can tell? I had to floor it and crank the engine to get it started.

But if all those parts were replaced, I have no clue what your problem could be.