Will the fact our passports are set to expire count against us or make the CoA application process trickier?
It could be tight with the timings if they do take 14 weeks, but in 14 weeks time you may not even need a COA! Not sure how quickly he can get his passport renewed, but I reckon it would be more important for him to apply for FLR(M) before his student visa expired because they will stamp FLR(M) visas in expired passports if you have a good explanation.
I know the waiting is nerve wracking but I don’t think it is time to start worrying yet. For the moment get all your ducks in a row so when it does come through you can renew his passport, register your CP and then apply for FLR(M) in short order.