I know what you are asking about as I had some of the same problems.
Mine would sometimes miss going into third all the way when shifted manually.
There are two things that are critical to the Pro Matic working well and one that isn't so critical but helps a lot.
1. The adjustment is critical (meaning when you move the shifter the linkage at the trans is exactly where it needs to be)
2. The self centering spring HAS to re center exactly for the mechanism to catch the next cog
3. (not so critical but makes a big difference) is that the cable that comes with the Pro Matic is 5 feet long and has some give in it, so it's not super accurate about position.
For #1 all you can do is verify each postion of the shifter vs the trans linkage.
Take the cable loose at the lever on the trans and put the shifter and trans in each position.
Verify that in each position the cable will slip right back into the linkage lever.
It may very well need some geometry changing.
#2 There isn't a lot can be done with the centering spring except to get a new one.
I bent the spring on mine slightly so it had the correct center for the cogs on the ratchet mechanism to line up EXACTLY, but it took some time and patience to get it right. (got it wrong probably 10 times before it was right, and it doesn't take much of a bend to make a big difference)
The slightest little bit off and it won't work right.
Also if you look close at the mechanism while up shifting manually, you will notice that the ratchet arm barely gets ahold of the cogged plate that the cable is connected to. (this is what makes it miss the shift sometimes)
I used a moto tool to take about .020 off that arm surface so the arm more positively catches the cogs on the plate.
Last but not least is the cable.
I found that one of the B&M cables for their ratchet shifter is 3 feet long and is EXACTLY the same except for two details.
It is a super heavy duty cable and has WAY less slop in it than the Hurst 5 foot cable.
The second detail is that the eyelet on the shifter end is 2mm larger around than the Hurst cable end.
A 2mm spacer sleeve did the trick here, and now that it is all done it has never missed a shift up or down since.
That used to drive me nuts.:D
The whole process was trial and error, but now I have super positive and accurate shifting with NO noticeable variation in cable position shifting up or down.
I works perfect every time now, and I attribute a lot of it to the new heavy shift cable.
