You might start with a 40' wood-ended reefer. You'd have the wood ends. You'd have to eliminate the roof hatches and ladders, add boxcar doors and build the inset fishbelly sill and grabs. The I/M one might be the easiest choice. Also check out mmagliaro's concurrent NP 39000-series box car build thread where he plans on splicing wood ends onto a wood side box car.
Jack Burgess says the B-50-1/2/4 that you're probably thinking of is 14" lower than the B-50-5. Per diagram in "Southern Pacific Freight Cars" Vol. 4, the B-50-5 is 13' 3-1/8" railtop to rooftop. So make it 11' 11" for the B-50-1/2/4. Guessing 4" or so for the lowest part of the exposed sill and with 33" wheels slightly covered by the sill, figure 3' for their combined height, making the wood body 8' 11" tall.