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I have most answers but don't quite understand the reasoning behind them..
48A Worked in a particular field,like unsuccessful
examinees?(8) P-O-G-E-. Ploughed?
9D One in severe ignorance initially supporting graduate teacher(9). M-H-R-S-I. Maharishi?
28D Organ part produced by churchwarden after audible complaint? (4,4) -L-E, -I-E. I initially had Clay Pipe but have gone wrong somewhere if 32A is Stablemate.

28D Organ part produced by churchwarden after audible complaint? (4,4) -L-E, -I-E. I initially had Clay Pipe but have gone wrong somewhere if 32A is Stablemate.
FLUE PIPE.

9d MA graduate HAR(I in)SH I ignorance initially
A MAHARISHI is a Hindu teacher
28d A FLUE PIPE is part of a pipe organ Churchwarden
refers to the pipe and influenza the flu'

48a Theyused to refer to someone who had failed their exam as "ploughed" the other meaning is obvious.
Hope these two entries have helped,
Best wishes,
Jerry

PLOUGHED is correct.
Apparently to plough also means to fail a candidate in an examination.