Encoding home videos for IPhone, AppleTV and IPod Touch

Hi Folks,
I'm on latest version of Compressor and FCP.
Objective: to encode home video transfers to a format that is suitable for AppleTV, IPhone and Ipod Touch - in an efficient manner (this is key)
99% of the videos would be VHS and camcorder tapes in SD format.
I mentioned efficient manner b/c I tried running and Iphone encode through the presets in Compressor for a 2 hour VHS transfer - nothing fancy, just 12 chapters. I'm on my 2009 quad mac pro with 8 GBs RAM.
The estimator through the 'share' feature said it was going to take over 3 hours before I quit. The other reason I quit is b/c it won't be compatible with AppleTV.
I created DVDs for my client so I tried handbrake using the video_Ts folder and it created an IPhone/IPod Touch file no problem - only 40 minutes. Not bad. I tried the Universal preset and QT gives me an error that the finalized file isn't compatible.
I guess my question is: does it matter quality wise, if I run through Handbrake vs compressor? For this particular client, there are 12 hours worth of videos to compress.
I know about setting up a cluster on my mac pro, but everytime I try more than 1 file in a batch, the subsequent files fail. I can't even set a cluster up with my 2006 mac pro either - yes, I've had discussions with FCP support staff and have tickets. It's a bug
So, any thoughts? 3 hours (at a minimum) seems awfully long to compress.
Of course, I would be charging my client for these videos, but at that length of time, I'm not sure what a feasible cost would be for both sides.
Cheers,
keebler

If you are send out self contained movies to be processed in Compressor with Standard Presets (no adjustment to frame controls) you should be getting decent speed. If you want I can try encoding a two hour DV clip. How far did the encoding get before you stopped it? The estimates are not necessarily accurate at the beginning.
Also if you can get the Clusters working (disregarding the size of the batches for a moment) should help with speed. I run into limits of around 20 per batch so make multiple batches. Not the most optimal way, but could be worth it to get them all going. Set them up for overnight and it should be done in the AM.
Creating off the Video_TS folder is compressing compressed material, so it could (should) reduce quality when compared to encoding original source material, though based on the quality of the source it may be more academic...
I would try to get the Compressor end working myself. (Ignore using share, just open Compressor and put movies into it.)

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