This is from my experience. Note that these instructions assume you have the common "top normal" type of RD. If "low normal," reverse the HIGH & LOW in the following.
Once you incorrectly install and subsequently attempt to operate the improperly assembled barcon shifter, you've got to get back to point A. Shimano's directions for installation of new barcons even instruct the user to not operate or fiddle with the assembly prior to new installation. Unfortunately, those same instructions don't describe what exactly will happen if you do fiddle with them or the procedure to correct.
To restore the lever range and indexing action, you use the "lever boss cover" as a *key* to wind the lever back to its original position. Merely rotating the lever boss cover to its correct position won't necessarily correct the problem.
From recollection, here's how I have done this:
1. Remove or disconnect cable
2. Remove the lever and boss cover from shifter body
3. Install boss cover in correct orientation
4. Put lever in place on stud or "axle", but in the LOW position; that is, with the lever nearly parallel to the ground.
5. With either the screw in place or with your thumb & finger securely holding the lever against the boss cover, shift the lever to the HIGH position.
6. Repeat this action, if necessary, until the mechanism is restored to its original position. You'll know this when it won't rotate with gentle force.
7. Install the lever in the HIGH position and secure mounting screw. You should now be able to operate the barcon through the full range of indexing detents.
8. Re-install cable and adjust tension as necessary.
Hope this helps.