In the hopes of getting a response, I'll list some of the better pathophysiology books I've found:
-Cardio: Pathophysiology of Heart Disease by Lilly
-Pulm: Pulmonary Medicine by Weinberger
-Nephrology: Renal Pathophysiology: The Essentials by Rennke
-Neuro: Neuroanatomy through Clinical Cases by Blumenfeld and Neurological Differential Diagnosis by Patten (not strictly pathophys, but they were pretty great)
The best GI book that I've found so far is from The Little Black Book series, but even that is more of a book to take on wards rather than a primary text. Costanzo's section on endocrine seems okay.