I've done some cursory searching through LLBA and have come up with a number of studies comparing the Japanese and Turkish grammars... there are undoubtedly many, many more, however. A brief selection of these studies follows (though I'm not sure how useful it will actually be, as many studies can be difficult to find copies of):
- Allen, S., Ozyurek, A., Kita, S., Brown, A., Furman, R., Ishizuka, T., & Fujii, M. (2007). Language-specific and universal influences in children's syntactic packaging of manner and path: A comparison of english, japanese, and turkish. Cognition, 102(1), 16-48.
- Demirci, K. (2006). Japanese compound verbs and their turkish counterparts: Verb+verb. [Japonca'daki Birlesik Fiiller ve Turkcedeki Fiillere Benzerlikleri: fiil+fiil] Bilig - Turk DunyasI Sosyal Bilimler Dergisi, 38(summer), 123-136.
- Ido, S. (2002). An alternative description of incomplete sentences in turkish and other agglutinative languages. Turkic Languages, 6(2), 157-191.
- Sener, S., & Takahashi, D. (2010). Argument ellipsis in japanese and turkish. MIT Working Papers in Linguistics, 61, [np].
- Simpson, A., Hwang, H., & Ipek, C. (2009). The comparative syntax of double object constructions in japanese, korean, and turkish. MIT Working Papers in Linguistics, 58, 41-62.
I've specifically tried to leave out any studies regarding the Altaic hypothesis as you requested. As for full comparisons of Japanese and Turkish grammar, I highly doubt that such a thing exists, due to the sheer scope of it all.