Tom,
The SIO device on the DX58SO2 board is NOT used for thermal monitoring or fan speed control. The SIO's SMIOVT monitors are of absolutely no consequence; on this particular board, the BIOS doesn't initialize them, most are not connected to anything and none of them have been calibrated. Thermal monitoring and fan speed control decision-making is implemented on this board using a standalone ASIC that is compliant with Intel's Heceta 6P requirements specification. Your board will have either an Andigilog aSC7621 or (more-likely) an ON Semiconductor/Analog Devices ADT7490. While both of these devices have their own unique set of capabilities and device-specific register set, for the "standard" set of capabilities that we define in the specification, there is a (more or less) common register subset and the devices are pin-compatible. These devices are accessed across the System Management Bus (SMBus).
Intel provides a Windows-based tool, called Intel® Desktop Utilities, that allows you to monitor the various temperature, voltage and fan speed sensors included in these ASICs. There are also plenty of third-party tools that can provide this support as well. Here's a non-exhaustive, randomly-ordered list:
AIDA64 (http://www.aida64.com)
SpeedFan (http://www.almico.com/speedfan.php)
PC Wizard, HW Monitor (http://www.cpuid.com)
HWiNFO32 (http://www.hwinfo.com)
Note that Intel does not validate the level of compatibility of any of these tools.
Now, all that said, there are plenty of reasons for system hangs and the thermal issues don't start until way, way, way far down the list. I am not saying that you are wrong; I am just saying that you are going to need to do a lot more to verify it. I am being skeptical because you haven't said anything that would conclusively point me towards a thermal issue ("hot to the touch" means absolutely nothing; there are always going to be components that are hot to the touch, regardless of the load being placed on the system). As well, your system description is pretty anemic; you need to provide more details. If you have any concerns regarding what you say in a public forum, you can send it to me via private message.
If you need pointers on what to include, here are some ideas:
1. What other components are plugged into your system? Describe all add-in cards, all internal peripherals (HDDs, SSDs, ODDs, etc.), etc. Do you use RAID or similar capabilities?
2. What changes have you made in the BIOS Configuration? Have you verified that you still see the issues with the BIOS configured to defaults? Yea, there are going to be cases where you absolutely have to have some configuration changes in place for a system to work. If so, document these settings! What is the O/S configuration? What software is (always) running?
3. What fans are being utilized? How many inlet fans are there and what sizes are they? How many outlet fans are there, what are their sizes and where are they located (top? rear?).
You mentioned a new heatsink-fan unit for the CPU - a heatpipe tower. I hope you picked one that provides cooling for 130W. I also hope that you are using one that (also) provides support for pushing air down onto the motherboard and providing cooling for the voltage regulation circuitry and the memory. There are many solutions out there that do a great job of cooling the processor but leave the voltage regulation components to slowly f. There are even some that, in addition to not providing airflow themselves, block much of the airflow generated by other sources....
As a first step, I suggest that you install Intel® Desktop Utilities. It will generate onscreen alerts for over-temperature situations and will track them until removed. I also recommend that you try version 3.2.6. This version has a lot of robustness and capability improvements over previous versions. While it is not specifically tested on DX58SO2 any longer, it still retains support for it and should work reliability (the DP55KG board also utilizes these ASICs and I have tested it on this). Version 3.2.6 was released to manufacturing just this past Friday. It may take a day or two for it to be made available in download center. You can use the previous version (3.2.4) in the meantime, but I recommend that you switch to 3.2.6 as soon as it is available to you. When you are installing, you will likely see a warning that the application is not being tested on this board; simply continue the install - and don't forget to reboot the system when it says to...
...Scott