Hi John,
A few thoughts:
RE AS29: In my humble opinion, the AS concept is one of the great maritime innovations of the last century. Bolger wrote that he thought the MANATEE was contending successor to the Herreshoff MEADOWLARK (a cruising design for amateur DIY). I consider the AS line to be very much more so, especially in the age of second growth timber.
RE Ease of conversion - I'm with Arne. Should be easy enough to convert the main to junk. The mizzen can be left as is (more on this later)... it's hard to beat for simplicity.
RE Balance - Phil (Bolger) is using his standard 'trick' in the AS29 rig. The mizzen is either all standing or struck. The main is designed with a diagonal leech... as you reef, the center of effort moves forward as area is reduced. Net effect is to maintain overall balance against the constant area of the mizzen.
To reproduce this effect, one of the junk sailforms with a diagonal leech would help. Quadrangular sails - such as seen on many traditional craft, Slocum's LIBERDADE, and Bolger's usual junk sail choice - seem to be off the JRA radar, but I'm not sure why. Possibly due to reefing geometry considerations mentioned in Hasler/McCleod? Pics I've seen of traditional boats so rigged seem to furl without trouble.
W avoided the issue on LUNA (AS31 following the AS29's lead) by using two large sails (cat schooner, in that case) which can be balanced against each other.
In practice, it's likely you can sail under well trimmed main of any shape (e.g., a Sunbird or Reddish sailform), and adjust mizzen balance via its sheets, under and over trimming as necessary. I think it will be a matter of nuance.
Conversions to JR often allow an increase in sail size, as it's so quick and easy to reef (Bolger endorses this approach). By adding balance and extending aft, you'll pick up considerable area over the original gaff rig. If the resulting aspect ratio seems low, you can always go up.
RE Mizzen - Consider a somewhat larger mizzen, especially if it must overcome balance issues mentioned above. We also wished we had larger one on LUNA to counter the considerable forward windage of the furled JR sail bundle, wind-cocked or at anchor.
Maybe start with a taller mast and Tyvek mizzen till you get a size that fits? Can always cut down!
We had great luck setting the mizzen with no haulyard. We fixed a light line at the masthead, led to a cleat low on the mast.
To strike sail, push the inbrd end of the sprit vertical (bring iits outbrd end down and to the mast). Roll up the bunt, and spiral wrap sail and sprit to mast using the light line. Cleat off and done. 'Whip' the line in high winds to get first wraps as high as possible.
RE Leeboards: We love 'em!
A retaining cable (our preference) or bar means you don't have to tend them between tacks (they become Off-Center Boards, rather than lee boards).
We find that they tend to perform better when placed further forward than I expect. In both LUNA and SLACKTIDE, we still have a little lee helm with sails trimmed for the wind and boards all the way forward. Have to crank some weather helm in with over trimmed after sail.
I notice board placement is far fwd in Thames Barges and many others of similar type... could be an effect of the very firm bilges?
Consider spanning bulkheads with your (leeboard) guards. We didn't on LUNA, and an... er... intimate encounter with a dock pushed the unbacked guard into the hull hard enough to crack veneers. Looks like the AS has plenty to choose from. Never hurts for the guards to go longer than necessary to reach the next blkhd... they make great boarding steps!
*****
Hope all this helps... good luck with the conversion!
Dave Z