So I have a issue with the TSA clearance, it states that my flight school has to verify the training.... I don't know what my flight school will be, I'm hoping, there will be none.
You have to do it at a flight school. You CANNOT do it with a private CFI as US immigration law does not allow this.
You will have to go to a SEVIS approved school ie. a 141 school.
There is no limit on the number of M1 visas you can have. As long as you meet the eligibility requirements and maintain your status you should have no problems.
This has been covered in much detail above. Please read the posts rather than just posting on the end.