I built a Fusion on a Mac Pro 2008 with Mavericks as i recall. It has performed flawlessly and got me around the small 120GB SSD limitations. In all, the boot drive was about 1TB and I didn't need to move much content to other drives (I have close to 1TB of Video\Music in iTunes, so I did keep that on extra HDD in the Mac Pro.
The creation of Fusion takes a bit of care, but follow the directions and you will be OK. I know several people who have gone this route without issue, and they were not particularly savvy users. You can pair the SSD (any size) with HDD (any size). You get the full benefit of SSD for boot speed and App loading, but also get the extra storage from the HDD without having to mess around with changing paths. Despite it being destructive (both drives will be reformatted in the process), it is well documented and works quite well.
Your TM backups can be of any (recent) version as long as it is older than, or equal to the target system.
I am a little uncertain about restoring 2 drives to 1 if you go the Fusion route, I suspect Migration Assistant would import only the user data that was on the old SSD, then you would have to go into Time Machine and Restore the data that was on the HDD to the new Fusion drive. Presumably you didn't move the entire home directory to HDD?
You might read over this site for some tips,
http://pondini.org/OSX/SetupOther.html, this site covers a lot of Time Machine topics. If your entire home folder was moved to the HDD, you might have to move it back to the SSD (along with the ~/Library folder), do another backup, then migrate. The contents of the documents, iTunes media etc would still be on the HDD, but you could then restore the HDD contents back to the Fusion drive after the migration is complete. Or, you might talk to an Apple Store Genius to get their advice.
Dual TM backups is not a bad idea. I use Airport Time Capsule alone, and have had no issues through two restores, but if your content is critical, by all means take the extra precautions. I have also done several restores from USB backups without issue.
One more word on the OWC. JBOD is fine for creating tons of storage space, but RAID gives you resiliency. JBOD is just like attaching a bunch of USB drives, any one can fail and you lose the data (unless backed up), but RAID uses parity (or mirrored images depending on which RAID level you choose) so a drive failure simply requires you to replace a drive and the controller will restore the data. In RAID5 or 10 with the 4 drives, you can get a massive amount of capacity with resiliency and dual TM backups will not be critical as the RAID will in effect create the resiliency. However, the whole thing is subject to catastrophic loss (fire, flood, theft), so an additional backup offsite is the answer if you want total peace of mind.