1. Lukewarm letter from Harvard < awesome letter from any other school. Point being, go where you will thrive because what's in your letter matters as much as the writer. Again, if all things are equal, sure, UTMB would be better, but all things are rarely equal, especially if you pick a school you will be less happy at.
2. Higher step scores are not any assurance that any individual will have a higher score. However, I will say I think that 1st-time pass rates say something really important about the curriculum because 1st-time pass rates mean that the curriculum has a universal boost for different learner types. UTMB is actually probably the top choice here because they pretty consistently have 100% 1st-time pass rates, which is amazing. That said, miserable student at UTMB will likely not do as well as a happy student at another school. Also, much like MCAT scores, above a certain point, step scores fall off the importance factor for a lot of residences. A really good example is PM&R. Just visit the PM&R forums and see how important personality becomes once you hit the avg PM&R step score. A miserable candidate with a high step score is not going to fare well on the interview trail.
3. This is true, but it is also research specific, so it depends on what you are interested in. Everyone at El Paso completes a research project, but you can graduate from UTMB without doing one. El Paso has no shortage of research and they have a massive new facility coming online that is going to greatly expand their research opportunities. Still, statistically, UTMB does have more research opportunities.
4. True, but with such a menial difference in residency program director ratings between the two schools, the chances of it playing significantly into the process are not great, especially if the OP goes somewhere that they are unhappy for 4 years.
At the end of the day, going someplace you don't like because you think some small differences in metrics will help you get to where you are going is silly. Even if you were talking about a powerhouse school like Mayo, if you are going to be miserable there because of something in their curriculum vs being happy somewhere else, seems like a bad decision, but to each his own.