Jim-
There are a couple additional possiblities you might check.  The CIS 
uses a separate cold start injector mounted in the intake manifold.  
These can clog, causing cold running problems, or leak causing warm 
running problems.  The cold start injector is controlled by a 
'thermo-time' sensor mounted in the coolant.  If these get out of 
spec it also causes gremlins.

Another more remote possiblity.  The crankcase breather enter the 
airbox underneath the CIS fuel metering valve; that big circular disk 
that regulates fuel injection quantity.  Problems have arisen from 
crankcase water vapor condensation freezing on the underside of this 
disk, weighing it down and causing fuel quantity calibration 
problems.  The solution?  Vent the crankcase to the outside.  
Additionally, plain, oily crankcase vapors can build up a sludge on 
the underside of the disk, gumming up its action and changing fuel 
calibration from the weight of the crud.

One more.  Bad grounds <shame on you.>  Jettas had a problem with the 
main ECU ground on the cylinder head being pulled off from the 
movement of the engine within its mounts.  Make sure you have an 
excellent ground between the ECU and the engine.

Hope this helps-
-dan