How sad nobody able to help with such a minor request, trying to get some advise on shift linkage, 29 looks no one can help
Jason... There were four entries on your initial post, one of which requested what engine you were speaking of, another asking if you were speaking of the shift rods within the exhaust housing or a shift cable. We still don't know exactly what specific linkage you're speaking of. A person needs to take the time to detail exactly what the problem is, especially when no pictures are forthcoming.
You did reply once, stating that the engine model was/is J15REOD, a 1995 15hp Johnson. I retired in 1991 so I am simply assuming that the lower unit shift setup is the same as the earlier models, and if so...........
However, assuming that your problem applys or did apply to the brass shift connector..... Only one bolt (normally the top one) should have been removed from the brass shift connector to release the shift rod.
If both bolts were removed, reinstall the brass connector to the lower unit shift rod with the bottom bolt, having the split of the connector facing whatever way it faced originally. Note that the groove of the shift rod "must" align with the bolt hole of the connector.
Pull the lower unit shift rod "UP" so that the lower unit is in gear so as to obtain the highest height of the unit's shift rod.
Move the engine's shift handle so that the upper shift rod extends "DOWN" as far as it will go.
It is now simply a matter of installing the lower unit to the engine "ONLY" far enough to align the groove of the upper shift rod with the remaining hole of the brass connector, then installing/tightening the remaining bolt, then after making sure the water tube is inserted correctly in the water pump, either turning the prop or the flywheel to align the driveshaft splines with the crankshaft splines to allow you to fullly install the lower unit.
If the above procedure does not pertain to the problem you were having, let us know exactly what you had encountered.