Ok, after having done the Subie conversion with the shift rod that went under the engine, after a while it didn't seem to be the complete answer and so I decided to do the cable shifter from www.cableshift.com and had it installed. It didn't seem to be too much of an improvement and so I decided to pull the plug on that mechanic that installed it and since my niece's hubby opened up a new shop, I thought I would have him take a look at it today to see if an adjustment would help.

After disconnecting the cables from the shift shaft and shifting into the gears by hand, he thinks that maybe something internally with the shift fork is bent?
It seems to be a mirror image of what it is doing when using the cable shifter to shift. 2nd and 4th go into gear crummy, either way. All the other gears work good, just those two in question. He advised me to have it looked at, and that the problem with the shifting probably is in the trans, rather than the cable shifter itself?

Click to view attachment

Old subie shift rod
Click to view attachment