The springs hanging and extra 3 inches below the axle shouldn't affect your ground clearance all that much. You're not going to go rock-crawling with it, are you? If you are, you need to rethink and keep the trailer tall.
This may sound goofy, but shorter tires will bring it down a little bit.
I'd buy some three-inch lowering blocks and bolt those in. Taking leaves out is not the answer. You're going to end up walking in the bed, and if you're springs are tired or soft, it's like walking in a canoe. I did the same thing with a '62 Ford box last year. Junk yard springs made it stable for walking in, and I mounted the housing up on top of the leaf springs (between the springs and the frame). It might sit a little high for my taste...but I'm not taking it to car shows.
-Brad
