Major Kudos to TG on his intake and port work. We got into a discussion on a different list that he was visiting and are now discussing some of the older 500-550 Honda engines. I have some of the older Yoshimura catalogs where Yosh was actively developing and racing the early 500. The idea of the 29 being too big for the engine is really a problem of air flow in the head and manifolds. TG did a good thing in straightening out his intake manifolds AND lifting the port angle by 10 degrees. The factories often begin an engine design outside of a frame limitation and then have to make adjustments to get everything to fit. The budget dollar often gets the final say in the design.
Yoshimura liked running the 31mm Keinin CR carbs and they probably matched the full race designs that Yosh worked with in their porting and hc pistons and race cams. The new Honda 150 single is running a 32mm FCR carb, but it also has a 4-v cylinder head and bore/stroke specs of 66 x 43.7. But understand that this is a dirt bike and not a highly tuned RR bike. Carb size isn't always the entire problem behind loss of botom end. The entire system needs to be balanced in order to make use of the big carbs. that means the ports, cam, and exhaust system needs to be optimized to work together.
Looking at TGs pics of his carbs, there is a small problem with the inlet design. Now, understand that this is a Production design in order to mount a rubber connector between the carb and the air filter box and it has a straight tube at the outer edge of the small diameter bell inside the inlet of the carb. The bell is nearly correct, and it would flow decent if it were cut off right there. But the bell is actually too small for the venturi diameter and a bigger bellmouth would work better. Of course, you get into problems with the various holes for idle circuits and bowl vents etc.... So basically it is a compromise that disturbes the flow. The non-smooth-bore design also disturbs and restricts the flow. There ARE inserts for some of the Dirt bike type Mikuni carbs that screw into the bottom of the slide and smooth the flow under the slide. Website for one of the products is here
http://www.startinglineproducts.com/catalog.cfm?pageID=detail&catalogID=1&catID=50&productID=892 Jetting adjustments would have to be made for the increased flow. There are some good articles out there on flow and bellmouth design. Here is a link to an article by Dr. Gordon Blair on intake Bell design
http://www.profblairandassociates.com/pdfs/RET_Bellmouth_Sept.pdfIt will be a little technical for some but there are illustrations to show how it all works.
Hope that some of these ideas help.
Swiss