Though for this particular professor, you may want to wait before asking him for a rec letter, for the others that you already know, you may want to ask them early, because they have other things to do as well, and other students who will wait till the last minute. The quality of of rec letter may be affected by your timing, and the time you give the prof to write the letter for you.
Normally, this question should be able to be answered in the sample request from the department you are applying to, but generally, they don't want a theses over 25 pages, (single space) because they have other students papers to read as well, unless your paper is extremely compelling, then go ahead. Otherwise, I don't think they are very particular in your choice of format, but since you will have to do it anyways, chose the format that is used in your field.