I was going to look at my notebook for the speedmaster last night to see what the issue had been, but totally forgot about about.
rummaging thru my memory (sketchy at best) it seems that the fuel level problem I mentioned was more related to the main jet bore height relative to the needle tip. It would be like shimming the heck out of the needle.

Will it hurt anything to leave them in? no reason it should, worse case it runs crappy and you have to change them out.

05 speedmaster - 1100cc, 11:1 racing pistons, Carillo rods, thunderbike cams, ported and polished head, 2mm over intake and exhaust valves, Barnett kevlar clutch, scepter pipes, oversize manifolds, 45mm HSR's, TTP stage 4 firestarter