If it is already warmed warmed up, then it's probably not the lamp output changing and you should not need to do any warmup passes.
Have you done an "Eveness" type scan? Easy to do with reflected light - set a sheet of white paper on the bed and do a scan and bump up the contrast to see where there is light fall-off and where the scanner "sweet spot" is. Kind of like testing your enlarge/enlarger lens for fall-off on the easel by printing onto high contrast paper. Not sure what you could put in the bed to do this? A piece of ND acetate? I suspect a sheet of Lee theatrical filter would work well for this.
Are you trying to butt the two scans together end to end? What about having some overlap and then feathering in the two scan? That could help hide any minor differences in density...
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