1.

Way back when I installed EB, I installed it over 1.6. (I had BI installed and just copied the folder then installed EB into the copied folder) Anyway, it has always worked. However, load times are excedely high when compared to Vanilla and after sometimes after I've played for a while, the game play actual becomes stuttery on the main campaign map. Is this a result of installing over 1.6 and not over 1.3.
No, this is just because EB is as extensive as it is - the engine wasn't really designed to process such large text files. If you want to get rid of the "stuttering," then the only options you have are to either find a smaller mod or upgrade your computer. I used to get major slowdowns after exactly two battles, and the initial splash and loading screen took over 8 minutes all up to complete (this wasn't too bad; I normally just spent this time doing something else). After upgrading my PC, the "stuttering" practically stopped and the loading times were cut down extensively.