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2002 Ford Focus Window regulator and motor replacement problem

I just replaced a broken rear passenger window regulator with a new regulator and motor I bought from an Ebay store. It works and was relative easy to replace, however, the window controls now work in reverse (up makes the window go down, etc.) and the window stops about 1cm short of fully closing. It is supposedly the correct part (2000-2007 Focuses require the same part). Is it possible that by reversing the wires (the part came with a connector with a red and blue connection) from the motor to the door control that the window may then close all the way and the controls be in the correct orientation?

I also compared the original part to the new one and the new one appears to be the same size, etc.

Reversing the wires is a good guess for the up/down. But maybe you can get some more info – Could you have plugged the connector inbackwards? Can you compare the connector wiring to the original wiring to see if they maybe got reversed? (On Dad’s 1962 Plymouth Valiant the rear turn signal lights were reversed left/right! I think QC is better nowadays, but maybe some aftermarket parts are still shaky.)

I have no idea if reversing the wires would fix the stopping point.

Only the adaptor that came with the part can be reversed (I plugged it in red to red and blue to blue). All the other connections have only one way to plug them in.

Probably 2 different issues. Reversing wires should fix one of them. If window is disconnected from the regulator, does it slide all the way up (close) without significant resistance? The window shouldn’t stop going up until it meets resistance. Make sure the track or door frame isn’t bent.