Head work questions

Ken;

Remove the dowels on the China walls. Where the intake sits on the block. RTV is my choice, the end gaskets are your call. Ether they fit and work or they don't.
On the retainer issue, the stock units in the exhaust side could be the rotor retainers. Toss them aside. IMO, for the cost of new retainers and locks, it's cheap cheap cheap, for an easy correct fit.
As far as springs go, I would have ordered the Comp springs with the cam. Cam, lifters, springs, retainers and locks come in a package deal from Comp Cams. It also includes a timing chain.

If there is a bolt hole misalignment on the intake to head, you can just hit out the bolt holes. A die grinder would do the trick. Use Sealent on the bolts. Not RTV but thread sealer/sealant. Thinner gaskets are possible if need be.