makenoiz,

I just keep a copy of the the layout_boxes sql create table code and do a find/replace on the site name. Then I insert the modified file back into the database and you settings will be the same for the new store. Just do a
Code:
mysqldump -u <user> -p<password> zencart_database --tables layout_boxes > layout_boxes.sql
When I'm not quite so lazy/busy I plan on building a little "setup" interface that will create the config files and insert the appropriate layout_boxes rows, but for now this is pretty quick.

I've been over this code pretty thoroughly with the modifications I've made to it, and haven't found anything introduced with this module that should cause any problems as the number of sites increase.

The only general performance suggestion I would have is to be careful how many products you put in a single category. This is a Zen Cart thing, nothing to do with MultiSite other than the fact that you may have more products than a single store. To give you some scale, with my dedicated MySQL server I need to keep the number of products in a single category under 5,000 for the store to perform adequately, which is highly unlikely for in most situations I would think.