You can browse the catalogs of e.g. Vishay or Sharp and choose a transmissive sensor (photo interruptor) with a smaller slit or aperture. They may have one with a form factor identical to TCST2103. Possibly the output current is lower, the load resistor has to be adjusted in this case. You can try to reduce the aperture of TCST2103 by partially covering the existing one. A possible solution would be a laser printed transparency film, that can be attached to the part.
However, after I know about the micro-stepping ratio of your drive, I fear, there may be rather a problem of drive position temperature drift and repeatability. The difference can be checked by performing repeatability tests with and without re-zeroing the position, I think.