Comprehensive Guide for Ph.D. thesis in Mathematics?
It could also be helpful to check this and this short guides and the books by Steven G. Krantz, in particular 


A Mathematician's Survival Guide: Graduate School and Early Career Development
A Primer of Mathematical Writing


The first one contains subsection 4.6 which deals specifically with writing a thesis, the second one is on mathematical writing in general but it does not really deal with the theses per se.