Joss,
When I fitted new cables last year (see
HERE), I found the same as you, that some undue force was needed to get the gear lever assembly back into the hole in the tunnel and bolted down.
The cables seemed to be hitting something, but I could not see any obstruction within the chassis tunnel. Once everything was connected and adjusted, I noticed that the cross-gate cable was hitting the sharp edge of engine where the engine and gearbox join. The outer cable was marked, but not damaged. By shortening the cable slightly, the curve of the cable is now away from the engine, and re-inserting the gear lever assembly into the chassis tunnel was easier (I did not feel as though I was forcing it).
As you say that you have difficulty finding 1st & 2nd because of cross-gate movement, this might be something to check.
John