Going from a cast valve cover to a stamped valve cover should be no problem. Your stockers will work fine.
When you get to the bigger heads (Stage-V Millenium, INDY 1RA-6, BAE, etc.) you'd need longer tubes. The tubes are all the same OD but there are many different lengths to the top o-ring shelf and then different extensions from there depending on the wire type (top seal) you want to use.
Indy sells longer tubes for their larger heads and so does BAE, but when I need something custom I contact William Bahl (btdt44@epix.net). He machines billet tubes with screw in steel ends, to your exact needs/specifications and doesn't cost any more either.