1. what are the SEO implications with Google as far as "Duplicate Content" is concerned? I would not like to see the original main site be penalized because of duplicating the site under other URL's. Does anyone have any experience with this or comment/advice?
If under same domain as sub directory, no problem. If different domains, yes, same content will hurt your original site. It would be best to modify your content if you are on different domains.
2. does this work with Snap Affiliate add-on module? any known issues or code modifications required?
Yes, work up to 1.3.9
3. does this work with Hidden Wholesale and Dual Pricing - Wholesale Pricing add-on modules? any known issues or code modifications required?
Work, no problem
4. is it possible to allocate a SEPARATE PayPal account to each duplicated site ?? (establishing separate PayPal accounts allows for individual site name in the shopping cart, on invoices, receipts etc.) - I see this as desirable to differentiate sites as far as customers are concerned.
Not likely, maybe you can work on different paypal Page Style, no idea does it work
5. can templates be different for each site (colors, boxes layout etc) ???
Confirm, yes you can have different template, different CSS on each site. that's the beautiful of multisite
6. can Specials, Featured Products etc be made different on each site?
Yes, base on your selection to display of categories.
I hope that some one could tweak and make a fully working one for 1.5.0
Thank you and just my 2 cents
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