It would be nice if the connectors weren't so confusing to pair. Additionally the following suggestion would likely fix a bug with these and AE2 autocrafting as well.

When originally crafted any connectors should have no group assigned at all.
Once placed in the world if the connector has no group it should be given the next available one.
If you right click with a connector on a connector in the world of the same kind, the whole itemstack in your hand gets assigned the group of the connector you right clicked. This should work even if the itemstack already has a group, effectively changing it's group.
To clear the group of existing connectors craft them alone in the grid.

This is WAY more intuitive than figuring out crafting recipes, and it means first crafted connectors need no special NBT data at all. That should fix AE2 not recognizing the item once it's crafted.

The current system certainly is unintuitive, unpredictable, and brittle

It's worth noting that if there is concern about abuse for having variable cards represent networks, then you could ALSO make it so there's a "private network" slot in the connector as well that makes it so if it's ticked then the network id becomes specific only to the person who placed the connector, or even make it so players can craft player cards that only they can craft so they could even share them privately too.

Additionally to head off any concerns at the pass, existing system already is abusable by just breaking another player's connector and copying it's group. This would actually FIX that if you go with the option of making it specific to the person who placed. Alternatively you could make it so there's a setting so only the player who placed it can open the GUI AT ALL thus completely obfuscating the network id. You could even have a slot for a list of users allowed to open the gui.

AND this would mean players wouldn't have to break their existing connectors just to add a new one to it. They'd be able to share with other players by simply giving them the network name without having to visit them and hand them anything, AND it would still be secure due to the security features mentioned here. It would be a MASSIVE improvement in intuitiveness and functionality.

I prefer the current crafting method at the moment. But I'll leave this issue open in case I'd change my mind in the future.

Regarding AE2, this is an issue on their end. They are not calling the appropriate crafting events, which ID depends on. They said that they wouldn't fix it. So the only thing I can say is not to use AE2 for connector crafting.

I'd like to take an opportunity to further convince you. There are two issues. One issue is that there's a little ambiguity in how the crafting method works. Currently if you place two connectors with different groups in the same grid it's difficult to intuitively understand what the result will be. Additionally the only way to make a new connector in an existing used group is to break a network in order to get the connector whose group you wish to make another connector for.

Another alternative to my method would be to use your wrench. You could right click any grouped connector to save it to the wrench and then once saved right clicking another connector would write that group to it. Sneak right clicking on nothing (or anything but an ID item) would clear the current group from the wrench.

I suspect there's a misunderstanding with the AE2 bug. The item gets crafted just fine. AE2 simply doesn't recognize the outcome of the craft. I believe this isn't due to using the wrong method to craft it, but due to AE2 needing to know the exact item that will result in a craft in advance of all crafts due to how patterns work. Even if we stuck with how grouping works now and simply made the initial craft result in ungrouped connectors until placed, I believe it would fix the AE2 issue. I've confirmed this myself by crafting the resulting 2 omni connectors i get from AE2 in an empty grid and putting them in. This resolves the craft freeze, because AE2 now sees the item it was expecting to get back.

I appologize for the lengthy reply. I should have submit two separate issues for this really. Also thanks for the quick reply :)

Related issue on AE2:
AppliedEnergistics/Applied-Energistics-2#3587

Alternatively, could you make it use an integer variable card to set the group ID and avoid having it set during craft?

At the very least it could be made blank on craft and set group when placing instead. Even if the right click functionality isn't put in and crafting recipes to matching things to group are left. Also the AE2 "bug" isn't a bug. This mod will never work with AE2 as long as it applied dynamic nbt data to the resulting crafted item. That's a huge reason this would be nice to change.

IT's extremely frustrating having this as one of if not the ONLY mods i ever run whose autocrafting recipe always fails.

This would ALSO benfit the mod because useless groups wouldn't be created on craft.

Frankly I ilike @IMarvinTPA's Idea except I'd prefer it was a String rather than a variable so i can name my groups. :D