Vavle stem height....

I have seen this on several heads also and it always bugs me. sst3193 has a point that if you don't pay for blueprinting you'll get this. If it's only a few thousandths (say no more than .030) the adjustable rockers will allow correct adjustment and it won't make much difference in performance. If it's over .030 it starts to make a difference on the geometry as you suspected. When it gets up to .060 it's getting pretty bad. I mentioned that because I had a set that were like that. I had to put lash caps on the intakes to make up for the shorter valve stem so it would have the correct geometry. Either that or take them back and pay for blueprinting or buy longer valves. The lash caps worked fine even though I know it's not exactly doing it the "right way".

I don't know why they don't sink the seats as far as stock but I do know that not sinking the seats in has a positive advantage on flow. The farther you sink the valves the poorer the flow. In my opinion it has to make a difference in power production from cyl. to cyl. when they are all uneven. Hope that makes sense.

BTW: I located a set of stock J heads to check the installed height because I couldn't ever find a figure as to what it should be. The stock heads measure 1.90" from valve seat to valve stem height. There was only .010 max variance with the stock heads.

Also if you disassemble them to clean them up you shouldn't need to worry about keeping the valves in the same hole they came from with no more miles than you have on them. You can try different valves in different holes to get the variance balanced out as close as possible because I'm sure the same amount of material removed from grinding the valves and seats are not always the same.