I have a couple of mismatches, early XS1 heads/camcovers, and will be facing the same challenge. Kinda cooked up a scheme.
Primary importance is the cam bearings (fore/aft) alignment,
Followed by flush (side/side) alignment at the cam bearing ends,
Followed by flush alignment of the valve cover openings.
Alignment of the rockers and valves is a given, they're aligned with the cam bearing openings.
I'd fit the dowels, and a cam with bearings. Lower the camcover onto the head, check for interference with the cam bearings.
If no interference, check the remaining 2 alignments.
If no fit, try again with just 1 dowel.
Else, remove the dowels, lower the camcover onto the head, align the cam bearing ends, check the valvecover openings.
I feel that the dowels may be considered unnecessary, since the bearings will establish alignment in the fore/aft direction. Use the cam endcovers to establish alignment in the side/side direction. Bolt it all down. Valvecover openings are on their own. Within limits, use gggGary's goober and/or o-rings trick. Else, remove valvecover studs, resurface the openings...