KDO I will try to help.
1. Stocking Bass in 1/4 acre pond - is it feasible?
Yes should be easy to manage.
2. It appears that 1' min of freeboard is required above fully flowing Aux spillway - what is min elevation between Primary and Aux (Primary is 6" PVC siphon)?
With only 7 acres of watershed I would design the primary to handle it all depending on the site and available space.
3. Is a 6500 GPH Mag pump ok for running water falls into the pond?
This video has a partial view of my water feature which is using a 3000 gph irriagtion pump.

As for size of pump it all depends how big and dramatic your looking to acheive. My pump will flow about a 1 to 2 inch deep stream about 20 inches wide.
4. Are falls a good idea, or would they cause too much turbidity? Mitigation possibilities?
Yes they can be used for aeration, Our leader Bob has written articles about this in the PB mag. He also talks about planting certain vegetation in the stream below or auxiliary pond to use as a natural filter.
5. Bottom profile: 8' max depth, ramping down to 3' - how steep should the transion be for 90' long pond (65' of bottom)?
With 3/1 slopes(the norm) a 90 ft long top elevation would make your bottom length approximately 57 ft long.
6. Liner: to mitigate risks, we think liner is important. what is proper way to cover liner given 2:1 sideslope. Would gravel or clay mix be better to ensure that it doesn't slide down to bottom?
I would contact these guys they are a PB sponsor. They are experts in the subject
http://www.coloradolining.com/gallery/gallery1.htm Posting pics of the site would help the experts help you.
Good luck
Rocky.