SCT PRP - How do I tune/adjust for IMRC delete and longtubes

[projectslideway]

I was able to get my car dialed in and running well using SCT PRP. I'm going to be adding my IMRC deletes and longtubes in the next few weeks. I was wondering if anyone could write up a small tutorial on the best method for doing each of these. It has been a learn-as-I-go process for tuning and I'm thinking I should do the IMRC deletes first, get the spark dialed and then attempt the longtubes and any transport delay/heater adjustments. My current setup is as follows:

1996 Cobra LLX3

Vortech w/intercooler
Blow-thru HPX
60lb injectors

Any advice is much appreciated, thanks!