Version used: 2.1.3-GTNH
It's currently impossible to change the stacksize of ghost items in recipe mode:

As you can see, the little widget to change it in the bottom right corner is not here. I messed a bit with NEI settings, and it's only possible to change it when NEI has the item giving ability (same result in utility mode with item giving ability disabled)

It would be life changing for mass reencoding AE patterns if this was possible.

while i was discutting with other players on delta, i found out that the workaround is only availiable for operators, as normal players can't use neither utility mode with give feature or cheat mode, as it's only availiable for OPs.

as a work around, simply switch temporarilly in utility/cheat mode, change the stacksize, then go back to recipe mode.