1. You need to find every place in triggers that call force players of player group "team 1/2", and change it to "custom player group 1/2" you dynamically create at start.
2. You need to find all initializations you make for players at start (if there is such) and change their event from "map initialization" to "ingame lobby timed out".
Not sure how big your code is, my bet is it's around 15 trigger folders with around 30 triggers each, searching each trigger will take around 15 seconds manually. so that's 15*30*15 ~= 2 hrs of time
On one hand that's quiet some time, considering you'd be doing a boring boooooring part, but on the other hand making the ingame lobby and fixing the worst problem of cc sounds pretty good