I came back from vacation and here are answers to your questions:

a) Is the baggage checked through by AA from SFO all the way to HYD?
Yes, My bags were checked all the way from SFO till HYD
b) Is the transfer from Terminal 3 (American Airlines domestic) to Terminal 5 (for Etihad) in ORD smooth and quick enough?
Yes, I took the morning flight and I had too much time in hand(You need to take air train to go from terminal 3 to 5 but you need to clear security check again in Terminal 5)
c) Ease of transfer in Abu Dhabi
Its 20-25 mins of walk from Terminal 3 to Terminal 1(where all flights to indian sub-continent start. Also, both outgoing/incoming flights to HYD had a remote stand, so you will be bussed to the planes and Business class had a separate bus)
d) Etihad's service and food onboard in Business Class
Its okay, I had vegetarian food and can't comment. There was good amount of booze and FA's were very friendly. Entertainment system is good with lot of options.

So I assume you used your AA Miles?

How many miles did the Business Class cost you?
How much did you pay in Fuel Surcharges and Fees and whatever extra they take your dollars away for?

I used 67500 each way, so 135000 miles in total.

Thanks for the feedback, concordian!

As I was looking to use miles to get the SFO-ORD-AUH-HYD tix for my (elderly) parents, decided to make it simpler for them and went with BA on SFO-LHR-HYD instead - apart from the 67,500 miles one way per head, BA business class seats cost $690 per head in taxes, fuel surcharges and fees :gulp:

JaguarBest, Etihad doesn't impose any fuel surcharges, so, apart from the ticketing fee of $25, my guess is the taxes and fees would have been in the $60 range.

You are right, it was $68.10 to be precise, so with $25 fee it was $93.10 total.