I don't have an LA but don't the liners on these have a locating pin? Apart from the fact that there are 3 non symmetrical and different shaped ports it would take a genius to put the liner in wrong

But having re-read that you totally dismantled the engine...did you put the rod back on the right way round? There's a chamfer on one end of the rod bush and it has to go on first so the chamfer is against the crank web.