Thanks for the help. So short term, >50 turns to the end of the game, you wanna grab one more tech real quick and ta heck with the long term strategy, do you run merchants or scientists? OR do you run merchants in wal street and scientists in oxford?
I'm not sure I comprehend the first portion of your question, but generally speaking I wouldn't mix specialists. I'd let the Oxford city run Scientists all the time, while the Wall Street city runs Merchants. It would be a viable tactic to use specialists in this fashion, though, even if it could mess up your plans as to what

you're trying to cultivate.
I consider the science/tax/culture/espionage settings (for

) to be the short term solution to whatever my current priorities are. So, if I really need the next Tech I'll max research until its done, or if I really need the money I'd rise my taxes until I've upgraded or what ever. Also, if I'm expanding rapidly it would take too much time to build both the Courthouse and the Theater in every new/acquired city. In that case I would probably just rise the

percentage temporarily until my borders have expanded everywhere. Or if I lack 1000 some

points to be able to perform a certain mission, I'd divert

to this aim temporarily.
But I could of course employ the corresponding specialists in my cities instead - if they are available. (I would probably need to build that Theater first in order to have a Artist specialist, unless I'm running Caste System.) You could try both approaches to see what works best - for you.
Lastly, is there ANY way to make it so that the specialists i select stay selected? or does it just reset whenever it wants? and if it resets whenever it wants, does it reset just before your turn ends or just after your turn starts? (i.e. does it do any good at all to reset my specialists EVERY SINGLE TURN, or does the computer just do what it thinks is best and change them right before i would get the benefits I want?)
I believe that the AI/governor assigns citizen duties between turns, and this happens whenever the city changes size or whenever unhappy citizens become content - and vice versa. You can cycle through your cities with the arrow keys once in the City Screen, or you can use the City/Domestic Advisor (I forget the actual name, but you can get there by pressing F1) to see what your cities are up to. (Click on a city name and you see what specialists are active at the bottom of the screen. Its kind of a hassle to actually change them in this mode, but its doable.)
I do believe that you can influence what the hell the governor is doing with your city, but only to a point. There's no point in telling him to prioritize

however, because then you automatically will get a Spy specialist (which actually generates some

) when its time to assign another citizen.
I've actually incorporated Great Spies into my overall strategy (for Tech stealing) - because I'm bound to get one sooner or later. The chance isn't that big for say 5 Scientists and 1 Spy (1/6), but when it happens I will have the required Spy units ready to deploy. When I'm not getting the surprise ninja character

the Spy specialist is actually helping me get out more Great Scientists, as the

points generated are valid for whatever type of

you end up generating. My problem is all the non research cities that waste citizens on Spy specialists. I really don't need those

points since I'm gonna use the inevitable Great Spy to infiltrate the enemy. Duh!
I, lastly, think that you could get some help with these issues by using some mod. I don't use these myself (for whatever reason) but they really sound super!

Read some previous posts in this thread for more info on these.