TRANSFORMER PHASING

The common links are the REASON you went ahead and got them all in phase to begin with. That process allows you essentially to have a real big transformer, comprised of all the actual transformers, with lots of outputs, and one common return.  This allows the use of outside rails to activate accessories and control relays that use a different "hot" supply, (might be AC, DC, higher or lower voltage, etc) while maintaining a "return" reference with the track common wire.

If you disconnect all the commons, you just have a bunch of independent transformers, and gain no electrical or logical advantage.

Keep the connections to the common bus.  You may have power without them... but follow the circuit... it would be a terrible imbalance on the transformer providing all the return current.

I believe your question is whether you need both the commons to ground bus AND the commons you used for phasing tests.  If so, the commons to ground bus provide exactly the same connection as the test commons, but the commons to ground are probably more robust.  If so, you can remove the test commons and use just the commons to ground bus.  (For those transformers, your connections from each transformer common to the ground bus should be no smaller than 16 gauge wire, and preferably 14 gauge.)

Thanks for the advice guys.  I have decided to keep both the transformer to ground bus connections and the cross connections between transformers.  I figure that whatever duplication exists will only make for a more reliable system and protection from poor or loose connections anywhere.