RTR manual if I recall when I looked through it just had RTR info, but heres some info:
scriptorium give your managers more scrolls and can help with retinue and traits
the effects for wonders is forever as long as you hold them
yes other families will attack (b/c they are the senate, not the plebes)
you probably had squlor issues in the cities when they turned. squalor is the biggest challenge in the game
there is no rhyme to the healing of plague
that strategy is the general concensus of how to deal with RTW. I use the saturn temple in all cities and never do communal farming...
once the city is prosperous enough, i destroy forums sometimes too to decrease population growth.... I also only use Town Watch in cities as it is cheaper
Also, the game is a lot more fun if you play every battle instead of auto resolving it....