“the base circle on the cam seems to vary by a couple of thousands. This is an aftermarket (stock replacement)cam.”
You’ve almost answered your own question.
If the top of the lobe is reduced then the base circle must be reduced too, in order to get the same relative lobe height.
Since the donor cam wasn’t worn equally on each lobe and the grinder probably removes a minimum amount of material the base heights will vary lobe to lobe.
“So, cylinders 1 and 4 are adjusted when at TDC but 2 and 3 are not. With the varying base circle on the cam it seems like the adjustment from cyliner to cylinder will not be the same.”
With 1 and 4 at TDC suppose 2 is at the end of the intake stroke and 3 is at the beginning of the exhaust stroke.
In that case #2 exhaust lobe is on the base circle and should be the same lash as half a crank turn later.
#2 intake valve is open.
Also, #3 intake lobe is on the base circle and should be the same lash as half a crank turn earlier.
#3 exhaust valve is open.
Turn the crank 360 degrees and the roles of 2 and 3 are reversed.
The actual base circle height doesn’t come into play.