Others may have a different opinion, but personally, I don’t think using both programs would be confusing—especially now that you have a basic idea of how they differ, and since you’ve already been reading Sarno and Gordon as well.
If the SEP feels emotionally intense, it seems reasonable to alternate it with a day from the Pain Recovery Program, or even to pause the SEP for a day or two to give yourself a break. Both programmes contain ideas and techniques that can become part of your mind–body/TMS “toolbox”; you can try different approaches and see what feels most helpful.
Neuroplasticity work and emotional awareness can complement each other. Understanding the pain mechanism, reducing fear, responding differently to symptoms, and becoming more aware of emotions can all help teach the brain that it doesn’t need to keep producing the symptoms.
Howard Schubiner’s latest version of his book Unlearn Your Pain also incorporates ideas from both the neuroplasticity and emotional-awareness approaches. You might find it helpful to read that later, perhaps after you’ve finished the programs—or at least after you’ve finished the Sarno and Gordon books you’ve already started—so that you don’t overload yourself with too many sources at once.
Bear in mind that it's best not to rush, because rushing can create more pressure—and that is the last thing our nervous systems need. It can take time for everything to 'percolate' through to the unconscious brain. Also, I’d say approach things with curiosity and self-compassion, rather than as something you have to get exactly right. No perfectionism required!