What is the difficulty level of JIPMER MBBS entrance exam as compared to AIPMT? Which are the best reference books for JIPMER entrance exam?

Honestly, there isn't much difference in the level of difficulty of the two papers i.e., NEET and JIPMER. Both the exams are based on NCERT although JIPMER occasionally includes questions out of NCERT Syllabus. JIPMER is relatively easy as most questions are small and simple unlike some complex ones included in NEET. 

To prepare for the JIPMER exam all you need to do is go through the previous year's questions, revise your concepts, and formulas, name reactions of organic, and most importantly remain calm throughout preparing for the exam.