Regular port Commando head clearances

Hello Mopar folks. I have my 340 in the machine shop having x heads swapped out for Aluminum reg port MP Commando heads p4876785. They called and said the engine ran bad and bent push rods and determined the pushrod holes need opened up. After that they called and said "you have a lifter ticking,did it do that when you brought it in?'' I stated no. I found a engine build on the net where a fellow buttoned up a 318 with a different head casting from some cop car and when he fired it up he bent push rods and colapsed a lifter or more than one and they were damaged,so he opened up the pushrod holes and went back at it. These guys did some porting and intake gasket matching on mine and removed the boss in the port runner that reg. port Commandos have when new.
Im looking for comments on what ive got here and the clearance problems with the pushrod holes. Thanks,,,,,,,Matt