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Originally Posted by bp944
-Should I go with a 5.3, 5.7, or 6.0L engine?
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4.8
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-Does one want to shorten the stroke or lengthen it?
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For a given displacement, a longer bore gives a more compact cumbustion chamber, which you want for thermal efficiency.
If you can make it work, GM Active Fuel Management (google it), aka displacement on demand, would be helpful.
You'll want a monster, granny gear, which will be completely unused in track work.
As others are pointing out, you want low volume ports and a low duration and overlap cam, which are, of course, not the way high output engines are normally set up.
An interesting, challenging, project.