By degrade, do you mean slower, or r/w errors?
I mean r/w errors but I doubt you'll ever run into that problems.
This is a very scary subject. Can I use my Deneb card to boot with the updates already in place from the start?
Do not use Deneb dma driver with A4000T! You must use PIO driver with A4000T in order to avoid problems (I think that even if you don't use scsi units you may run into problems too if you use deneb dma driver due to the way A4000T is designed).
I'm confident with SCSI and willing to buy new cables and active terminators just to be sure.
scsi works pretty well on classics, you won't regret it.
I'm just about to buy one of the GVP 4060-DT's from Software Hut assuming they still have them (I think I may have had some CPU card issues)
IIRC latests GVP versions like that one are very reliable and memory access is faster than cyberstorm mk3/ppc too.
Is that controller reliable?
I think you won't have any problem using FFS. IIRC there were some problems using other filesystems but only if you tried to boot the OS from them.
I'm pretty paranoid at this point, like I said, I'm not using a full 4GB with 3.9 on SCSI, IDE and USB right now and they are all disastrously bad.
Is the RAM of your accelerators/motherboards OK? is your cabling ok?*are the drives ok?
What scsi.device do you suggest using for the onboard 4000T? I assumed 3.9 was the good stuff and that tweaking all the devices and libs would be a bad idea. Sometimes you can tweak them into instability, you know?
3.9 is just a collection of patches (and some of them are not very reliable). The most interesting parts are newer workbench.library, icon.library, updated scsi.device and newer FFS. If you own a Deneb you can extract the 3.9 modules and update the ones you need like scsi.device (there's a nice patch on Aminet done by Chris Hodges, the author of Poseidon), once you have updated the files put them into Deneb's flashrom.
Do you know what I should use for the GVP 4060?
An ide hd connected trough an IDE-SCSI adapter and ROM3.1 with the few interesting 3.9 parts (workbench.library, icon.library, filesystem.resource, scsi.device -and a4000T scsi device if you use A4000T-, ffs and perhaps updated shell). Skip 3.9 Reaction preferences when it's possible too.
Dump AmiDock and use an updated ToolsDaemon, it's faster, more comfortable and overall better.