So I decided to do it manually, and painstakingly set the blades purposefully a little low (this takes forever since a minute turn on the adjustment screw will throw it off). Then after tightening the blade the final alignment was about .004 above the outfeed table.
Is this close enough? I spent about a day on it and have bandaids on all my fingers :-) so my thought is this is good enough. I could try to move the outfeed table up .004 but my fear is that its likely to end up worse and I'll just keep fighting to get those last thousandths.
Will having the blade .004 above the outfeed table have a measurable affect?
I'm jointing some long 10' boards and before this did have a problem with both ends of the board being narrower than the middle. I'm checking both the jointer and tablesaw to try to get rid of this. Thanks for this and the other great advice I've gotten on here.