We could use the temples (of which you can only have one per city) to be used to represent a dominant guild/industry in each city. Thus weponproducing citie could have Weponsmith and armourproducing cities armoursmith, and other cities whatever they were famous for or had as dominant industry. Thus we could also ditch the blacksmith tech line.

I like the idea of limiting money flow, but how will we do this exactly? We could lower the overall fertility or trade benefits or we could simply make troops more expensive than in RTW. Where basic archers may cost 190 in RTW we could make them cost two to three times that in CTW and keep the overall money scheme relatively unchanged.
Yes, lower trade benefits, raise unit costs, and don't include farming upgrades, I think.

On training times: Maybe we could have zero turns for levies, one turn for professional troups and two or more turns for troops who have been granted land (eg knights). Thus restructuring of the society to get more knights and similar would require long time, while you could get levies in an "emergency".