I am not a flooring person, but a builder, and if I am understanding your situation correctly.
I would suggest to cut/saw the joist down, if the depth of the joist is not compromised in its weight caring capacity, there are charts one can find on the web, or building code, to see if the reduced depth is adequate for the span it is carrying,
I would snap chalk lines and saw it with a skill saw, and on the ends use a reciprocating saw, tacking a 1x4 on the side of the joist could be used as a guide for the skil saw, to make a straight cut across the length,
If the depth of the joist is below specs, double up the joists with new sistered joists to the old one's.
and then use a plywood for sub floor,
using construction adhesive to sister the joist up with, and to lay the sub flooring down and using screws can help in reducing squeaks.
jsut as in any building project the better flat-er the sub floor is the better the final product will be.
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