Hmm few questions there. Bear with me as I only have experience with the Jap diesel version but I'll try anway.
Oil: How much oil is in there? You mentioned it had 3 bottles of oil in it. How large is each bottle? I'm not sure of the exact quantity required in a 1.6, but it shouldn't have much more than 4 litres in the sump (sorry i'm unfamilar with US standards).
Auto: I assume this auto is of the electronic type. Does it shift correctly? By this i mean can you feel a proper clunk/ noticeable change in revs with each gear. So if you're gentle at around 20km/h (13mph), 50 (32), 70 (44) you'll feel a dull thunk as the auto shifts each of the 4 gears. These speeds may be a bit off, but you get the idea. Next, does the auto kickdown? This is where if you give the throttle a good stab while driving the auto shifts back a gear. So say you're on the freeway at 100 (63), the auto will be in 4th (overdrive, the top gear) with the engine at around 3000rpm, you stab the throttle, the auto will thunk back into 3rd and the engine revs will jump up. Of course this works at any speed.
All this is so we can see if the auto has any actual problems or if it works normally. If it does seem to work normally, you can reset the computer(s) and see if the error code comes back. To do this you disconnect the negative battery terminal, then press and hold the brake for a little while to discharge any remaining power. After a minute or so reconnect it. NOTE:
this will also wipe the settings on your clock and radio. If you have the factory radio, it may have a security code. If so, you will need this code and how to put the code back in afterwards. Also if your car has an airbag it may bring up a warning light etc, one of the US guys can chime in here. After resetting the computers (do these have a separate trans computer anyway?) you can check it for codes. Look in the stickies for instructions on how to check.
Power windows: Does the window go up and down very slowly but is otherwise ok? You can try lubricating the slides and mechanism with some silicon spray, you may have to remove the door trim to do this.
Anyway, hopefully the auto is okay. If there is too much oil in the engine drain it, and refill it with the correct quantity and grade of new oil (a good excuse to familiarise yourself with oil changes!) Another thing that would be worth checking is the spark plugs. Have these been changed at all? This is quite easy. Grasp the large end of the spark plug lead at the engine (not the lead itself!), give it a good twist and pull to remove it from the spark plug (do them one at a time). Next with a socket set use a T bar, extension and spark plug socket on the back of the spark plug. Loosen the plug and undo it (be sure to keep the socket straight so as to not damage the spark plug). Remove the plug and check the condition of it to this:
Carefully screw the plug back in by hand, make sure it's in the thread correctly, be sure it's not cross-threaded (most important!!). Tighten the plug by hand until it's finger tight. Then with the socket give it about 1/16 of a turn (no more!) if it's too tight the thead may be damaged.
Hopefully this will help find out what's going on.