Chris,
A couple of points: Did you slug your bore with pure lead (cast bullet alloy will give you an oversize result) and measure the slug and the Lee bullet with an
OD thimble micrometer that resolves ten thousandths? Most calipers are only repeatable to within a thousandth and I've seen some off as much as two thousandths. They are simply not adequate for bore and bullet diameter determinations. If you blow $14 + S&H on the one in the link, it will be a tool you can use with additional calibers, at least. (Don't forget to wipe its anvils off and check the vernier scale's zero reading to subtract from your final reading before making each measurement.)
Second, the tests I've run show bullets about 0.0015" to 0.002" over groove diameter are most accurate, but the bigger sizes seem to matter most to revolvers and lever rifles. For a self loader, 0.001" over groove should be workable, especially if you are having problems with chamber fit.