1. What make a frame/fork comfortable over bumps for long periods of time?
A long wheelbase. Long chainstays to keep you in well front of the rear bump center and a slack HTA with appropriate offset on the fork. The further your weight-bearing contact points are from the bump centers of the wheels, the more comfortable the ride will be. You also don't want a bike that is too laterally stiff. A little BB sway helps comfort. Strange but true.
2. What makes a bike track easily vs. quick handling?
A combination of HTA, offset, and acheived trail. If you're looking for a loaded touring bike, a lower trail number helps offset the slowing affect front panniers have on steering and helps make the bike more stable when you're climbing at a snail's pace. If you want a stable sport bike, then shoot for a trail of between 57 & 59 depending on how much weight you have on the bars (positioning related).
3. Do long chain stays hurt climbing ability?
Not directly. Excessive lateral flex in the chainstays/BB and lack of traction hurts climbing ability. If the rear end is appropriately stiff, then it's just a matter of keeping the rear wheel loaded to maintain traction. Think MTB'ing. As far as excessive lateral flex, look at it this way: if you used the same stays to build a bike with 440mm chainstays as you do with 405mm chainstays, you've significantly increased the bending moment on the stay without increasing its stiffness. Appropriate bridging can help here, but the answer is to use tubes appropriate to the load.
4. Does seat tube angle depend primarily on your anatomy, or will different angles acheive different things for a particular person?
STA should be dependent on your fit & knee to pedal spindle preference criteria. Different angles do have an effect on bike design, at least from a custom frame perspective. A slacker STA will, if your body move with it, will move your CG rearward. A steeper STA moves it forward. A slack STA requires longer chainstays to maintain the appropriate CG. Steeper STA requires shorter chainstays. STA angle also has an effect on cockpit length.
5. Do curved seat stays really have any effect on comfort?
Depends on the design. If you take seatstay out of pure compression then you can start to achieve some movement. It helps to have a pivot point, but introduce enough of a bend in the stays and you will start to achieve some compliance. A nice, fat, set of tires at appropriate air pressure helps too.
Any other issues or comments would be appreciated. I'm thinking of a custom frame, and want to be fully, but objectively, informed. I don't trust builders to tell me everything, as they seem to say whatever suits what their style is. Thanks.
You say that like you think they'll intentionally mislead you. Why would you buy from a builder you don't believe in? Better yet, why would place more belief in the opinions you read on the internet vs. those of somebody who earns their crust by working to achieve the answers to the questions you're asking?