Head Gasket Sitiation (6.0)

[ZeCaptain]

Hey fellas. I am a new diesel owner looking for some help with a head gasket complication. The truck is a 2003 F350 with a 6.0. I am doing a little refresh job, new egr cooler, oil cooler, head gaskets and arp studs. I had the heads cut because they had a warp in them and ran into a problem reinstalling the dowel pins. My 2003 originally had 3 pins on each head one on the 1st, 2nd and 5th bolt holes, 6 total. The 2nd hole has shorter dowel pins. After the shop cut the heads the dowel pins in the 2nd hole will not fit into the head side, no shoulder left. My new head gaskets from ford came with 2 regular dowel pins and 2 step dowel pins?(I am thinking the step pins could be a conversion from 18mm to 21mm?maybe) From what I understand the newer trucks only have 2 pins, one in the 1st hole and one in the 5th. I was considering just leaving out the pins on the 2nd hole all together, not sure if that would be a good idea though. Thanks in advance to anyone who can help me out.