M,
The paste height is what you establish it as. You're probably using a laser measurement system, and these depend on where your reference datum is. Some will measure from a silkscreen, a trace, or solder mask. These add height, not to mention HASL plating, because your 0 point is now about a mil or 2 over. Your USL should generally be around 1.5 mils over your foil thickness, so for a 5 mil stencil, 6.5 mils is about right as your target measureent. Then you go about .5 to 1 mil over that. Lower spec limit should be around 1.5 mils less than your target, so a reading of 5 mils for a 5 mil stencil is still within spec.
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