I,ve been following this thread & am a little confused to whats causing the problems
as dave has suggested photo,s would be good
With regard the column extension going past the diagonal...to solve this I made my extension "stepped" so that as it passes that diagonal it gives plenty of clearance .
I,ve used a group 4 coupling at the rack end & then used the triangular Ford part at the upper part of the column extension to where it joins the column that goes thru the bulkhead ( not sure if that makes sense

)
cheers
andy