It should be perfectly flush, this is a German built/engineered vehicle
after all!  The only adjustment for this is to move the strike plates on
the B and C pillars.

For a perfect seal you may need to replace it, it may be hardened into
the contours of the original bus and not match yours.

Many fun filled hours can be spent on this little task!
--
Stuart MacMillan
Seattle

'84 Vanagon Westfalia w/2.1
'65 MGB (Daily driver since 1969)
'74 MGB GT (Restoring sloooowly)

Assisting on Restoration (and spending OPM):
'72 MGB GT (Daughter's)
'64 MGB (Son's)

Stripped and gone but their parts live on:
'68 MGB, '73 MGB, '67 MGB GT