Thanks for the update Steve.
You have two separate issues:
1-the overheating
2-the stuck shrink
1-Is your 323 a rev-C1 box? Did you notice at what speed was the fan turning when the drives get too hot?
Did you tune the 'sysctrl' settings (Services->System, sysctrl, Configure) for your environment?
On the 323, the difference between the system temperature and the drives temperature is not that different, while in the 320L it might be up to 10 ºC different. As the fan speed is controlled by the system temperature, which is read at the box bottom main board which is cooler, on the 320L it is possible for the fan to turn too slow or even to stop, while the disks are hot and needing for a higher fan speed.
That is the reason why the sysctrl webUI as an option to "also take hdd temperature into account" checkbox (if the 'hddtemp' service is running, Services->System, hddtemp, but there is a catch, disks will not spin down).
In the event that you had "stop all services" (System->Utilities), then sysctrl is no longer controlling the fan speed, but for safety it leaves it turning at half speed. That might however be insufficient to cool the hdds when they are working for a long time.
So, I can understand why the boxes become too hot if you didn't anticipate and tune the fan speed control accordingly, e.g., setting it to always high, or adjusting the fan speed trip points for your local environment.
I have checked the shrink/resize code and there is nothing in it that might by itself cause the overheating, other than generating more heat for a long time from the disks than usual. The fan control or speed is not changed.
2-Regarding the stuck shrink operation:
Have you shrunk the partition (Disk->Partitioner) after the first successful shrink (*NOTE*)?. If you have, undo it by enlarging the partition first (doesn't need to be set exactly to the original size), then enlarge the filesystem (enlarging the filesystem is a fast operation). Then shrink the filesystem again. As now there is enough space in the filesystem and you have deleted files, perhaps the shrink succeeds.
If you have not shrink the partition (*NOTE*), I can only advise you to try to do it on a linux computer with a more recent resize program version (e2fsprogs). It might be a bug deployed for some particular reason.
NOTE: your posts are a bit ambiguous regarding RAID and partitions. If you have the filesystem on a RAID, operation sequences are a bit different: shrink filesystem -> shrink RAID -> shrink partitions. The enlarge sequence is: enlarge partitions -> enlarge RAID -> enlarge filesystem.
If you have not resized the RAID nor partitions, there should be no need to play with the raid, there should be nothing wrong with it, but only logs/configuration could tell.