Any ideas on how to approach them rebuilding the city and making themselves the kings- as it were?

Have one of them get forged documents of Nobility. Have them shore up the walls with timber and stucco to create the illusion of stone.

The cleric will likely want to build a temple. The wizard a library

Make it cost them, these are money sinks. And make it slow down city progression.

Things of that nature- but how should I count all of this towards collective resources? Time, money, materials?

They're gonna need to map resources in the area. And establish trade routes.

Maybe they make passive money from taxes after all is said and done?

Yep. Tithes the peasants.