I wonder if that's what's wrong with mine. Mine has been a real pain since day one. The strange thing is that it will shift into 1st and reverse pretty easy when cold but as soon as it's good and hot it's much harder. Most times I hit 2nd and then into first. It feels like the clutch isn't fully releasing or the pilot is trying to turn the shaft from misalignment or something. I have the Con OFE 13" clutch from SBC and it came with the re-drilled flywheel for the larger clutch. The other strange thing is that it didn't shift any better with my previous clutch, which was an SBC Con OFE 12. 25" with a modified disk hub for the larger input of the 5600. Makes me wonder if there is an alignment problem with the transmission itself. I even replaced the hydraulics with no improvement. The friction point seems perfect.
I do really like the gear splits, I just wish it shifted a bit better.