if the phone is already hot, better switch off the phone and let it cool down normally. I afraid rapid cooling from 50C repeatedly might do harm to your phone... if u put your phone there before it gets hot then it should be ok..

anyway, what aircond vent u are talking about? car aircond? do u mean ur phone gets hot inside car? if u put your phone on dashboard or anywhere inside during hot day, and inside your car is very hot, then the temp can go over 50C as well..

maybe u can try force stop recently installed apps first before do factory reset.. if u r lazy to install back everything.. but factory reset is the easiest to know whether its software or hardware problem..

Bro silent_stalker, if I was you I wouldn't take any chances anymore cause high heat will eventually kill you phone.

I rather do a backup apps+data, since you have rooted your phone and go straight for factory reset and wipe cache.

Or you may want to wipe cache first?

Anyway do backup first..

why do u want to change motherboard if it has no problem so far.. i know ur warranty is going to end. but maybe ur phone is one of the phone that is not affected by SDS.. later change mobo, got one that is prone to SDS. that is a risk also..
or better let ur phone die first so SC cant check warranty void or not? 

Warranty start the day you buy and end 12 month later in between change parts under warranty except accessories