"Are we any closer to identifying the owner of this box car?"
From the July, 1946 listing of Auto Cars with Type "E" Loaders with 8 floor tubes. All 40 footers except for the SP series:
Central Vermont 42000-42124
CGW 80400-80798 (Even No.)
SP 69555-70029 (50')
Most have notes regarding exceptions within the series, but that's a start. I'll leave it to others to narrow it down (if possible).