It matters cause there really isnt alot of point upgrading a Auto, unless your doing it for show, you cant turbocharge it or anything like that. However since your going Manual it might be a good idea to build it up to be turbocharged, since everyone at some point wants one since your building from the ground up you should take the chance to build it up, Pistons, Rods, Port Polished Head, etc. etc. Its not really that simple to just do it, but in theroy since your starting from the ground up it the best time to do it. Unless of course you just want a working engine again, then just stick to stock, and engine with 44k on it should be fine the whole way around unless it locks really beat.