I noticed that most of the recipes for making the chains are 3 similar blocks in a vertical line. This is similar to the vertical slabs recipe for Enchanted Vertical Slabs mod created by enchanted-games. Would it be more appropriate to have 2 iron ingots around the block of choice or have 2 blocks around 1 iron ingot?

Recipe conflicts are bound to happen. There is no way to avoid all recipe conflicts. Instead, use a mod like Polymorph which allows you to pick which recipe you want.

Would it be more appropriate to have 2 iron ingots around the block of choice or have 2 blocks around 1 iron ingot?

I don't really like having to use iron to craft chains for arbitrary blocks.