After acquiring my 26" frame and a few other components, I began reading this forum and beginning to wonder if I should switch to 29".

I am 5'9" tall with longish legs (no, I do not have legs that grow from my arm pits). I read somewhere that one should not consider 29" unless one is more than 6' tall.

A full 29" would not be possible now due to the frame that I have ordered, plus the height advice.

What about a 96? Since I have not ordered the fork so it is possible to switch to a 96. How would the 96 differs in handling from the 26"

You read wrong. Or at least it was written wrong.
96 doesn't affect fit over 29".
There's a halfbreed FAQ on this forum, all you ever wanted to know.

I'm 5'7" and my 29er fits like a glove!! If you 29er the 26" front (with a sus. fork) it will slightly raise the BB height...I think. Overall, if you had a non-suspension correct rigid 29er fork well I think that would make the measurements stay close to the norm...whatever that is. Good luck!