Minecraft block detection for a specific block

You'll need a redstone clock with a command block as shown below:

In the command block add the command /testfor @a[x=400,y=4,z=Z,r=600] and start up your clock. When ever a user is at that location, the red output line as shown in the picture will power. Once they have left the position, the output will power off.

I put together the following command system, all of which are in a repeating command block

This does not guarantee activation order. You should be using Chain command blocks to clearly define the order in which command blocks are activated. In the following image, the Repeating block is activated first and then follows the arrows in the Chain blocks:

The Chain blocks must be set to "Always Active", and you can stop the clock by stopping just the Repeating block. You can do this either with physical redstone or using /blockdata to shut the clock off:

/blockdata X Y Z {auto:0b}

It seems that the issues comes in with the order of the replacement redstone blocks being placed

There is a specific order in which the redstone blocks are placed via the /fill command, as well as the order in which redstone mechanisms are activated around that block. In this guide, the following image describes that order:

The numbered spaces around the redstone block is which block gets powered first when the redstone block is placed. /fill follows the same pattern when creating redstone blocks.

You should no longer be relying on this type of activation and instead use Chain blocks. Block update order and /fill order is not guaranteed to remain the same.