I think I have a blown head gasket. I took the heads off and two rods feel out. Why are they different and which holes do they go into the block?

Make , model year would help.
Did you do a compression test before dissembly?
What made you think you had a blown head gasket?

Ones aluminum the other is steel
The aluminun one goes on the exhaust side

Make , model year would help.

I would verify, Intake is colder than exhaust, exhaust may be steel and intake aluminum. I think both would be aluminum if it wasn't for the heat.
I Have seen people with oposing answers on this , A Manual shou make it clear? Good Luck?