Hi ARMac!!
I would suggest cross posting your problem with the game slowing down to Saz's Techie Help Desk thread if you have not already done so.
EMPTY BOTTLES: First continue to explore the Serpent temple. As I recall I found many more empty flasks than just three so you might just find more. How did you "use" the three you found? You only need one flask of Spider Nectar to do the ritual that will open the Naga Head. You might check Xignal's walkthru at
http://www.volberding.com/WHints/index.html it may indicate where you will be able to find more.
IF after further exploration you are unable to locate another empty flask - email me. I can hack you one.
Wyv