Well, you are running v2009 actually - v40 are only OBJECTS, but EXE is 2009.
It has always been recommended to upgrade at least the EXE to newer version (so called technical upgrade) as far up as license allows (and technology - you can’t go further than 2009 with v4 objects as there’s no more Classic Client in 2013).
Regarding tune some stuff - there is always something you can do to improve DB performance. I can’t name nothing exactly referring your case, but go through DUG’s SQL Server forum, or better get it’s moderator’s book and read his blog, if you’re seriously intended to squeeze out the most of your system.
If someone knows about NAV-SQL relationship & how to improve it, then it is Jörg - it’s not an advertisement, it’s a fact [H]
Finally, doing your technical upgrade you’ve already improved system performance, getting rid of SIFT tables - read more on this again in Jörg’s blog. BUT - that doesn’t mean there’s no more left to do.