John,
It does sound like the main may be too full, and this will certainly make for more weather helm once boat becomes a little pressed (around 12-15 knots TWS upwind).
This might be a silly question, but have you maxed out the outhaul? The purpose of the outhaul is to remove draft/depth from the section of the sail just above the boom (or add some by easing it from max tight for some conditions). The point is that you should be able to get the foot very flat when the outhaul is pulled tight-assuming the sail is built correctly (and mistakes do occur).
First, let's see where the clew of the sail should be on the boom with the outhaul maxed out. If your boom has a mark, tape or painted line near the end of the boom, measure from the back side of the mast right by the gooseneck, holding the tape near the back end of the boom. The forward side of the tape or line should equal the E dimension (from the back side of the mast). If there is no mark, add one by placing a mark or piece of colored tape right at the point equal to your E measurement, which is the length of the mainsail foot. If you have a standard rig 29, this should be 12 feet. If you have the Tall Rig, there were 3 booms. 9.2,9.9 and 10 feet-Most were 10.
Now that you have located the spot on the boom where the sail should be with the outhaul maxed out, go ahead and max it out. Your description sounds like the only part of the sail that is unusually deep in just above the boom-and there are basically 2 causes for this. 1). The outhaul is not tight enough, so you are not getting the foot tight enough to flatten the sail as a result (you will notice the clew is somewhere fwd of the mark), or 2). The sail is too long, so that when you max the outhaul you have not pulled the foot tight enough to remove the draft.
To really answer you on the sail shape I would need a photo posted, but let's make sure you are getting the foot tight enough and that the sail fits the boat (you may also want to check your sailmaker's records and ask them what E dimension they used to build the sail..Once this is established we can go from there. Of course, if this is as annoying as you imply, check the Rake, try removing an inch or so of aft Rake and see if this helps. Also follow the suggestions about weight I gave to the 25 CB guy.
Having said all that-an overly full main will make matters worse. I would not say the 29 needs quite as flat a main as the 25 CB-but by the time you have over about 12-15 knots TWS, you should have the sail as flat as it can be-it will be faster with less heel.
The Foss rudder mod is GREAT, but this is not what is causing the problem. Let's get this resolved, and then add the rudder to make the boat point higher, go faster with more control, etc...
Fair enough?
BTW-no argument with treilly on the "order of things"-Thanks "t"!
Seth