Lakewood knows they have a problem, so they sell offset bushings for you, the customer, to correct their product.
When you're set up to check bellhousing runout, check the rear surface of the bellhousing to make sure it's parallel to its front face. If these surfaces aren't parallel, the transmission will be cocked in relation to the crankshaft, causing the transmission to jump out of gear.
As with the dowel holes, these surfaces should be square, but frequently they aren't. The only way to correct this problem is to rig the bellhousing with shims or remove the bellhousing and have it surface ground at a machine shop. While at it, I would overbore the dowel holes, insert them and rebore them to make the holes accurate.