How to get the most expensive items into bottle caps?

You have to break high value items down into a combination of caps and other high value/low weight items that you can sell for caps to other merchants (or to the same merchant once they get more caps in stock). Post-apocalyptic economies tend to be heavily weighted toward the barter side of the spectrum.

It’s part of the game that there is a certain amount of wastage when you’re bartering; otherwise the bartering skill would be completely useless. Certain things requiring caps is also part of the game to make those things more valuable than an inventory full of random junk. You have to work for those things a little bit.

I believe most merchants reset the caps they have available if you stop talking to them and start the dialogue again. (if not, they should refresh over time)

As far as where to trade, I think Zack from the Gun Runners in the Boneyard refreshes about 3500 caps.

Only other option is to trade for some stuff like ammo as well as caps.