By installing the jamb nuts you'll lower the shifter arm. Might gain some travel.

 

Jam nuts will keep the linkage rod from twisting. Use a little loctite with the acorn nut to keep it on there.

 

You can also use a self locking nut in place of the nut you have on it now. If you are talking about jam nuts on the rod take the hemi joints off and get the right size die and cut a few more threads.

 

I still think you're not getting enough throw because your shift rod is to short and you're half-in/half-out of the shift position. If that makes any sense.

 

the overall length of the shaft determines where the peg on the shifter lies. lengthen and the shifter drops, shorten and the shifter rises. On the other hand, don't go too long or too short or you may invite other issues. I replaced and put hiem joints on mine... and jam nuts. solid feel.

 

That is not totally true on a Harley since both threads are right hand. The rod should be long enough so when the actual shift lever is free on the transmission, the other end should go on the other end so there is room so that end does not hit engine.
The actual position of the toe and hill shift is obtained by indexing it on the serrations. However there is some adjustment that you can make by not screwing the rod all the way in of course but on end need to be removed from lever to do this.. Most of the time on a Harley, it should be screwed half way in and locknuts used.
On my Yamaha, it has left and right hand threads like a turnbuckle so minor lever positions can be made plus of course the serrations can be indexed..

 

"Constant mesh" transmission. That means the gears need to be spinning ( meshing) in order to positively shift.
The shifting mechanism only needs to repeat it's same travel for higher gears.
DO NOT JAM ON THE SHIFTER. Shifting fork damage may occur.

 

Or you can remove the lever from behind the primary and move both the heel and toe levers at once. I don't like to disturb the bolts and or splines on the shift levers if I don't have to.

 

I just installed a new linkage on mine and I think I had the same problem as you, would get up into 3rd but would not go higher. To fix the problem I installed the end that connects to the shift lever in front of the shift lever. Try mounting it in front and see if that helps.

 

Work is consuming entirely too much time this week - I will endeavor to troubleshoot one evening this week when I get a break.

In the meantime, I agree that the length adjustment is off somehow. Though a test ride should confirm. How would moving the front heim back to the outside (based on the original measurement of the rod with the stock joints) affect the shift that much? The effective length difference cannot be that much.