Time has somewhat passed since the original post, my setup has changed and I have neglected the video input side as I have been dealing with single frames taken from a cine8 scanner.
Now, I had problems with Arrays, my A500 (StorEdge) was too noisy and my T3 (StoreEdge) was just utter crap. So I resorted to a temporary solution of just sticking a disk internally. Not the best solution at all.
My other issue at the time as to why it was dropping after a period was the audio and I had to either stop recording audio or reduce it's quality iirc. BUT.. I have a third Octane that copes with the audio and it's just a matter of applying the recorded file to the video track and syncing (the hard part).
I have since then purchased two nice array systems, a genuine Discreet array RS1220 and a Network Appliances DS14 mk4 which I have yet to install. I don't currently have the space to do anything, I've been purchasing a lot at the moment for an up and coming project and I have boxes and bits all over the place.
Anyway, as bad as my current setup seems, I decided to record some VHS (PAL) and see how it went after you posted this. It dropped at frame 4,596.
So, I'm afraid I can't direct you at the moment, it sounds like you have a great setup there, I have been thinking about getting Hyperdeck myself and also maybe a Blackmagic Aten[?]. Also think I will separate my SD & HD between two Octanes so I don't have to jig stuff about.
Oh and as for syncing etc, I do have an AJA Gen10 HD/SD Sync generator, not used it yet, but I also purchased a few pro SVHS boxes which can control the sync which proved much better than a home VHS player.
So, I was at the beginning about to record from my PS/3 at 720 (restricted by the size of my monitor) rather well in the early days, but that was a long time ago now.
And now, well all depends if my project goes forward I suppose, or I get a bigger house as I'm a bit stuck currently to just turning these on too heat the office.