Adam,
This sounds like a similar set-up as the 360 outback gear flap system.  The vary nature of welding makes it difficult to keep the end plates square and flat.  I had a similar out of parallel condition, so the torque tubes themselves could not be used as a guide for installing the bearing blocks.  I got a copper pipe of the same diameter to set the blocks.  This will make sure the torque tubes are axially aligned even if the flanges are not parallel.  If tightening the bolts at this point causes a lot of binding then a wedge shaped shim could be added.  Note that if the bearing blocks are set with a non-axial tube the binding is much more severe and will vary with orientation of the tube.  If the blocks are set with a truly straight reference the binding will be minimized and uniform throughout 360 degrees of rotation.

Another topic pertaining flap torque tubes - corrosion.  The platting on the interior will not be nearly as good as on the exterior especially towards the closed end.  Over time I found corrosion on the interior, and I live in a hot and dry part of California.  I pulled the tubes out and cleaned the interior with a round stainless wire brush mounted on a long extension.  I ran it up and down the tube until all the rust and loose plating was remove.  There was a lot of loose plating.  I then coated the interior with white gloss oil-based Rustoleum.  With white glossy interior walls, inspections are much easier.  If any rust reappears it will stand out like a sore thumb.

Chris Zavatson
N91CZ
360 std