SOMETIMES but not always, i have a hard time going into second gear, and on the way to work this morning 4th way the same(my "down" gears). other times it goes in like butter. is there an alignment for the shifter to transmission like the old muncies or something, or does the shifter just bolt right into the top of the tranny? i've never been inside one of these and have no idea what it's like.

 

There is no adjustment. The shift forks sometimes wear or the shifter pivot into the top of the trans may be worn.

 

You can try and change the fluid.

 

I am running a 3.0/5-sp and I find once in a while I get a bad shift but I am always low in the rpm range. If I bring the rpms up higher when shifting it shifts fine.
Not saying this is your problem but something to think about.