So I've been through this once before. Picked up a free bike that had a bent wheel. Disassembled the wheel and got the (steel) rim bent back pretty straight and then rebuilt the wheel using the old spokes. Somehow the spokes were too long and I had to file off the excess. Got it pretty true and sold it.
Now I have another flipper bike with the same problem. I went through the same process (which may be my problem ). Disassembled, straightened rim, rebuilt with old spokes, spokes protruding a good 1/8"-1/4" through the nipple. What am I doing wrong?