TLTD, when you said "if you're in Pro Tools just run everything into your IR loader", you are referring to the following?

Guitar->11R overdrive->11R amp->11R delay->11R reverb, then I run Pro Tools, insert MixIR2 as plugin to load 3rd party IR. FYI, MixIR2 is the only insert i run in Pro Tools. Hence, MixIR2 is sitting in the last signal chain, and 11R delay and 11R Reverb are sitting between the amp and mixIR2.

I am trying to mimic the real world setup where delay and reverb pedals usually sit in the effects loop of the amp.