I cannot begin to imagine how an increase in RAM would have any effect on temperatures inside your case. OK, you could argue that there maybe a physical restriction, and the RAM is blocking the airflow, and/or, the extra power required to run the RAM is causing more heat, but I think that would be highly unlikely.
The pertinent point is, are all the fans that are within your system working properly? That includes the power supply fan(s), which has a significant effect on overall cooling, the CPU fan, which if not working, is likely to fry your CPU in very short time, and any additional fans, such as on the graphics card, that may be required for local cooling. You should note, that if you are fitting a CPU to your new motherboard, you should have a heat transfer medium applied between the CPU and Heat-sink. this can be in the form of a pre-applied patch on the heat-sink, or you can use a thermal paste such as Arctic Silver.
If you have the correct fans fitted and working correctly, there is no reason to doubt the computer will run in a stable fashion.