After watching all thirteen OAVs, I'm still left confused by everything.

Anyway, I need names...proper or accepted spelling.  Most on the characters
of the second series.  Plus, if you could tell me what the hell was going on
in the last four episodes, it's a great help.  Also some questions...
1. Are Lady Funaro and Misaki both from Earth?

No, Funaho-sama is from Earth. Misaki is Jurain. 

(Line from OVA 5, "The emperor decided that the first wife should be  a
foreigner, and the second, Jurian"). 

2. There are four gems, right? Three on Ryoko (well, two were still on the
master key) and the last on Ryo-ohki, right?

No, there are only three total. The one on Ryo-oh-ki's head is a way
for him to interact with Ryouko, not a gem (from the 101). The "fourth"
gem, is a week varient Ryouko creates, which is blown away when TEnchiken
cuts her hand in OVA 1. 

3. Who is Lady Tokimi anyway?

Tokimi is the most powerfull of the Three Megami's. According to the 
Souran, the Memgami's were sent into this universe for some unknown reason. 
Tokimi is also probibly from the future (since there is wreckage from 
what is obviously Jurain tree's strewn about in OVA 11).

Pet Theory, Tokimi is actually Tenchi's daughter. 

4. The name of Yosho's space tree?  What's his other/earth name?

He named it after his mom, Funaho. His other name is Katsuhito, which,
interestingly enough, Washu still calls him in Manatsu no Eve. 

Keener, you really should make a FAQ on TM.

I started a pretty good FAQ a few years ago, but havent had the time
to work on it. 

Oh, of course these data are relevant to the Tenchi Muyo! fanfic I'm writing
for my eventful return into fanficdom.  Any help that you can extend please
do so privately.

Feel free to e-mail me with drafts/or qustions...

Thanks in advance