Ok, so quite a few days have gone by and I thought about telling you what I have been doing.
I have contacted the three universities and in each one the process is very different. I have had a lot of sleepless nights due to the amount of emails I receive though the night, but I must answer them ASAP to speed up the process. I have had to pay a lot of attention not to mix the emails. I doubt KyoDai would like to receive and email intended for Waseda.
UNIVERSITY #1, KyoDai:
First of all I contacted once again the professor I had talked to before applying to tell him I passed the preliminary selection. I confirmed with him all the information to send him my documents and he, once again, told me he wants me to apply directly to the Masters.
The International Office also contacted me to verify my interest in the program and tell me about the admission process.
Since the deadline to submit the LoA to the Embassy and the admission results date are different, the have offered to send me the LoA with a note that says I am going though the admission process and that, in case I am admitted, they would tell MEXT about the terms of my scholarship.
UNIVERSITY #2, Doshisha:
After contacting with the Office of International Students telling them about my intent on getting a LoA from them and to also clarify a couple of questions I had about their own formats. They requested that I have and interview with the professor I requested.
So the interview happened at around 4:00am for me, and I am sure we said a lot more than I can remember, but at the end she congratulated me for my research topic and said I would soon receive the LoA.
UNIVERSITY #3, Waseda:
So, again, I contacted the International Office to clarify some questions about the process. They answered really fast and also told me to wait for them to contact me in case they decide to issue the LoA, but that I should not contact them again.
I hope all goes well with Waseda, since there was no previous contact nor did they ask me to contact my requested advisor. I don’t know what would happen in case I don’t get one of the letters. I don’t think I would be given the option of looking at a 4th university since the placement preference form has already been send to Japan.