"...so for my custom rifles I should have the gunsmith cross out the old chambering and stamp the new one in..."

NO! Your gunsmith will probably already know this but he should totally remove the previous caliber marking . This will leave a small flat spot that may or may not be used to stamp the new markings. The serial number markings should not, however be altered in any way, as this is a serious crime in the U.S. It is permissible (and recommended) to stamp/engrave the same markings in a more accessible location if hidden from view though.

As for clearing security when traveling... not enough can be said regarding knowing proper requirements and being prepared for them before leaving home! These rules are changing constantly and what worked last time may not work today! Know the rules, have the right paperwork, make sure your firearms and ammunition are properly marked, be courteous but not a wimp while dealing with the security staff and above all... don't be in a hurry!