Hub gears don't function 9change) after taking off back wheel and replacing...

I have a hub gear system built by Sachs (now SRAM). The manual is here: http://www.sram24.com/newtechdoc/english/consumers/ghs/pdf/spectro/Ins_sram_S7_8_2005.pdf (manual differs from my system in that my gears are controlled by a lever, rather than a twisty thing and in that there is no window in the shifter housing.
After taking the rear wheel off, to get to the smooth brake-pad centre, I am unable to get the gears to function again. I accidentally left the gear in 3 instead of 1 when I took it apart and then switched to 1 before putting it back together (probably should have left it in 3). Anyway, when the shifter housing is removed from the the shift rod/tube, the gear lever moves freely between all gears, however when the housing is replaced onto the shift rod/tube (as in the instructions) then the gear lever moves either between 1-5 or 1-3 (I get different results each time I take it off and put it back). It's also more difficult to move than it used to be. Can anyone suggest how to resolve or investigate the problem further?