Aftermarket shifter in a stock console?

I started out with a B&M shifter using a cable ,it worked very well. The only problem is the cable is subject to heat and wear and the outside casing will rub as you shift if you don't secure it well enough. i went back to the OEM linkage. Mine was missing pieces on the lower linkage ,replaced it with 5/16 rod from Home Depot. Linkage is pretty simple to work with you just have to play with it a little. Sounds like your lower shift linkage is out of adjustment.Theres a slide nut on the lower push rod ,for adjustments. Even if the bushings are worn it can adjust to work. Your tranny shift finger is positive it dosen't move unless you move it. If indicator is not lining up I would say check your lower horizontal shift bar.