MedPuck:
...I did nearly the same thing. When I applied I was 95% sure that I wanted to go to a D.O. school. I wanted my interviews to fill in the last 5%. I applied to several M.D. schools in Texas and several D.O. schools. I was/am very interested in the MPH dual degree option offered by many schools and that narrowed down my choices quite a bit. Anyway, I am a non-trad and had about 9 years of civilian and military life I wanted to cover. I actually had 2 M.D.'s, 2 D.O.'s, 2 P.A.'s, 2Ph.D's and a Hospital Chaplain write me letters. They were all people I worked with or shadowed...except for the Ph.D's, they were my physics and organic professors. Fortunately for me, my undergraduate pre-med office acted as a focal point for the letters. They collected them, attached a cover letter, and mailed copies to the schools I applied to. No one complained I had too many letters (see below regarding MSUCOM).
...Just in case you are wondering, the subject came up in several of my interviews about applying to both types of schools.... On the Texas application, you have to list all other schools you are applying to. In two of my M.D. interviews, I was actually the one who brought it up. I just wanted to see how they reacted. Neither one of my interviewers (one was a Harvard grad) had anything negative to say what-so-ever. They encouraged me to explore my options and choose which best fit me. They both pointed out that there was staff/residents in the hospital that were D.O.'s. If I remember correctly, I think it was brought up in three of my D.O. interviews. I basically told them that I thought it was smart to keep all options open.... No one had anything negative to say what-so-ever.... Personally, if any interviewer/admission committee would ever hold such a thing against a student, I would seriously question their professionalism. Going to medical school is a life-defining event; to not explore all of one's options would be irresponsible and ignoramus.
Anyway, to answer your questions directly, I do not think anyone will hold extra letters against you. However, I can only speak regarding the schools I applied to. I would go ahead and have them all send out letters to all the schools you are applying to (except MSU-COM, and any others that have stringent rules)
...MSU-COM has a unique supplemental application. It asks you to complete a detailed listing of your work, volunteer, etc. activities, in addition to asking you to answer 5 essay questions. My supplemental typed on MS Word, single spaced with 10 "times new roman" font was 5 pages long. It is a monster and I saved it for last. As far as letters go, they ONLY accept 3 and one MUST be from a D.O. They MUST be completed on the form they send you. Moreover, it is pretty detailed--one of the D.O.'s who filled it out for me said she spent an hour on it and thought it was the most anal thing she ever saw. The persons who fill them out for you MUST know you very well so they can quantify their comments. MSU-COM, once you are deemed academically qualified, places the weight of the world on your supplemental and your letters. The last test is two 45-minute interviews. The interviews are extremely friendly and laid back. I interviewed in October and was the only one there that day. They interview often and try to keep the groups very small. I walked into the medical school and saw a sign next to the door to admissions that said "Welcome Dale Jackson, applicant for the 2005 Class." I saved about $500 by arriving on Saturday for a Monday morning interview. Three students who shared a house let me stay at their place. I met several students that weekend and I must say, "I have never met a more friendly group of people." The experience completely sold me on the school.
Hope this helps