Just to cover all the possibilities...
When you added the active heat sink, did you clean off the old heat sink grease and use new compound? The old grease was probably a lot like chalk.
Your symptoms just sound like such a good fit for heating problems.
Oh, just read more closely about the freezing happening during disk exercise but not during CPU exercise....
What does your SCSI bus look like? Are there additional items connected besides the internal hard drive? Is the internal hard drive properly terminated?
Also, the Macintosh provides termination power, so do not enable Term. Pwr. on the drive. That can cause problems sometimes if two slightly different voltage regulators get into a fight.
Finally, you aren't using a NuBus SCSI card are you? I had a Turbo601 upgrade in a Mac IIci way back when and there was some issue with SCSI Manager loading multiple times. I think the firmware in the SCSI card loaded it and the ROMs on the Turbo601 loaded it, and then things got wonky.
There was some way in one of the control panels to stop one of the two from loading it.
I don't know if they're still up, but there were a couple of great sites that supported these upgrades. You might have to use the WayBack Machine. Something like "The Unofficial Turbo601 Upgrade Site" and a similar site for the Quadra upgrades. I forget Daystar's name for that line of upgrades, which would replace "Turbo601" in the name of the site.
Ah, a little googling. You want The Unofficial PowerPro Homepage.
Wayback to Turbo601 page:
https://web.archive.org/web/20040415022708/http://www.brinnoven.co.uk/turbo601/macosiss.html
There's a section called "Eccentricities, Bugs and Solutions" that has a section on SCSI Manager.
Let's see, LowendMac claims to have duplicated the PowerPro Homepage here:
https://lowendmac.com/2016/the-unofficial-powerpro-homepage/
But I don't see any of the sub-pages. I would try to track it down on the Wayback Machine.
Hmmm, okay here's the page on the Wayback Machine:
Wayback to Unofficial PowerPro Homepage
It looks like there might be some interesting stuff in the "Message board" section assuming it got archived.