Does anyone have any sources on a conclusive guide to when the name "Yisrael" is used and when the name "Yaakov" is used in the Torah in reference to Yaakov Avinu, the individual?
From Here: http://www.aish.com/tp/i/moha/48955486.html
The Main Points:
Rashi  suggests that the name Yaakov indicates subservience, while the name Yisrael indicates strength and victory. Varying uses reflect different aspects of Yaakov's personality that come to light in varying situations. Another view is offered by Meshech Chochma, who sees the different names as expressing the distinction between Yaakov as an individual versus Yisrael as a national identity. Thus, according to Meshech Chochma, God addresses "Yisrael" exclusively when, and only when, there are national issues at hand. 
The Netziv  proposes that the distinction is between a supernatural aspect (Yisrael), versus a more mundane name (Yaakov) used when natural events or actions are described. Because humans cannot function purely on the spiritual plane, both names are needed.
Each of these suggestions seems to point to an unresolved tension in Yaakov's life which results in a dual identity.
 Rashi Bereishit 35:10, this idea is echoed by Rabbenu Bachya 32:29.
 Meshech Chochma Bereishit 35:10.
 Ha'amek Davar Bereishit 35:10, see Rabenu Bachaya 47:29 who see Yaakov as a name indicating physicality, and Yisrael as a name indicative of the spiritual.
I recently saw a commentary on the verse from the Book of Numbers
lo hibit aven b'Yaakov v'lo ra'ah amal b'Yisrael...
which says that Yaakov refers to the guf (body), and Yisrael refers to the neshama (soul).
Unfortunately I cannot remember where I saw it.