Someone will have to check my math on this, but something in the recesses of my brain tells me that the Shimano bar end shifters with the silver body and black rubber tips are 10-speed Dura-Ace specific and don't play well with anything other than 10-speed Dura-Ace, at least for indexed settings.
As far friction goes, however, my baseline assumption would be that that ought to be fine, of course.
In one of your photos, you show a lever attached to the thumb pod with a screw which I believe to be different from the stock one that comes with the levers. Again, I may be mistaken about this, but I think the Shimano levers need the screw they come with, in order to function properly -- I think it balances the friction tension more evenly, or somesuch. I don't know for sure but it's something to try.
Other than that, I don't know. I've used Shimano bar-end shifters in lots of different iterations and haven't ever encountered issues quite like the ones you are describing.
Gotta ask: what is a "long pull derailleur?" I've never heard that term. Some derailleurs surely have different pull ratios, but that is usually only a factor with indexed shifting. It might result in a slightly different feel, when in friction mode, from one derailleur to another, but it shouldn't be the root cause of the problems you are describing, from everything I know.
Maybe try going back to the stock bolts, and then take a look at the other factors already suggested -- is there a bind somewhere in your cable routing? Etc.?