With all due respect to your proven knowledge and skills
Firstly you need to start process of eliminations fella. Download ML and make the stick. Once down power off the Mac lean it with the access panel up pull sled 1 out with your HDD inside (along with any other drives inthe sleds) and plug the 840 directly into the sata plug where the sled connector goes in. Unplug all unnecessary USB devices. Power up, hold option to boot from USB, erase the entire volume using Disk utility off the stick and install ML on the SSD clean and see what it boots like after with just the 840 plugged in. If it's quick then power down and install the Solo X2 empty, then another cycle with the 840 in the X2. Then repeat the cycles putting your populated sleds back in one at a time.
Once you know the X2 and the SSD and disks in the sleds aren't the problem its no longer a hardware issue, but your OS X boot volume itself from your original HDD that's causing the slow boot. I have yet to see any X2+SSD not be much, much faster than a single spinning disk booting in overall times. Though the initial bit is slower it spanks the spinner after the Apple logo appears.
Been a busy day here in rainy London will be back to have a peep how you've got on mañana!
It seemed to me your suggestion of doing a clean install of ML on the SSD was more destructive of the current workable state of the SSD than I wanted to attempt at this time. I researched my last proposal of partitioning the HD and doing a fresh install of Mountain Lion on that partition and testing the boot time. I felt that was not destructive and more easily reversible. So I proceeded with that plan.
While booting from the SSD, I created a 250GB partition on the 1TB HD using Disk Utility. I downloaded a fresh copy of the ML Installer from the App Store/Purchases to the SSD. I installed the fresh copy of ML in the new partition and restarted after the setup procedure was completed.
Here is the previous timings data in Reply #18 when booting from the SSD:
Before repair permissions
logo - 27 seconds
spinner - 32
desktop - 160
After repair permissions
logo - 26
spinner - 32
desktop - 153
Not a significant difference
Here is the timings data for boot up from the new partition on the
HD containing only ML:
logo - 10 seconds
spinner - 17
desktop - 44
A significant improvement, especially when compared to the boot time for the SSD.
My conclusion is that this is a software problem - either corruption of a system file or a software incompatibility. - and not a hardware problem. Do you agree that the data supports that conclusion?
I would like assistance in arriving at a reasonable course of action to isolate the software problem. My preliminary plan is to use migration assistant (which I believe does not move the system files, but not sure) to move all the current data on the SSD to this fresh partition. I will then test a restart and compare the boot time to the data above. If it is unchanged, then it was a system file corruption. If it is back to the prolonged boot times of the unpartitioned HD, then it was a software compatibility with a non-system file.
Do you agree? Then I would REALLY need assistance in trying to isolate which software it was.
On second thought, would it be better not to migrate applications for the first boot test which might avoid installing some conflicting application files into the system file area? Then, if no slow down occurred again, finally migrate the application files?
Thanks for all your time and input.