It will be a mix of components, yes, everything from 0603's to IC's of various types to MOSFETs of various package sizes, one large pitch BGA component ( 0.65mm )
I've tried in the past cutting up a single stencil into multiple sub stencils, but as user mentioned above, it deforms the stencil pretty badly and not a good experience.
I do understand about defects on these boards from multiple reflow cycles is a possibililty. However with a total of 5 boards that will be used in-house only, the external exposure to people outside the company is not an issue. I will have to live with the possibility of having to debug something that may have a defect and replacing it. In my experience working with a similar board used in a similar setting here, I haven't had any issues reflowing or reworking sections of this PCB.
Thanks for the suggestions everyone.