Have three 2/4's cut - 1 for each end of the organ console to sit on, 1 for the back of the pedalboard to sit on. You might need one more for the front of the pedalboard if it does not sit in notches on the console.

Then cut two more and rout out holes for the feet of the bench, for use when a visiting organist needs the height.

This will lower you 1.5 inches.

If your console cannot be raised, get a good carpenter to remove the feet of the bench, remove the extra height for you. Reattach the feet, then have the carpenter create several sets of slighter large 'feet' from wooden blocks that have two short, fat tenons that fit into sockets drilled into the feet of the organ bench and into each other (i.e., the bench feet have sockets drilled into their bottom surface; the extra feet/blocks have the tenons on the top and corresponding sockets on the bottom).

The church where I work has a single-manual tracker (i.e. console and chest all in one, permanently attached to the floor) which needed to have the bench accommodate three differently-sized organists when it was first installed, and adding or subtracting height in 1.5 inch increments (three additional sets of blocks) has worked splendidly for 20+ years. The socket/tenon arrangement is very stable, and visiting organists very much appreciate the ability to customize the height from very short to quite tall. (Dealing with the flat pedalboard is another whole issue. :-)

If pictures would help, just let me know.