Looking to trade my bed caps for Gen 2 stock bed caps 06 Tacoma

I’ve had 16ga steel bed and tailgate caps on my truck for the past 6 years. I just got a bed cover and repainted them with 2 part epoxy liner to make them look brand new and nice with my new cover. The problem, I just found out, is that they are slimmer and slightly differently shaped than the stock and the bed cover doesn’t seal.
Looking to 1 for 1 trade bed and tailgate caps for stock ones in good condition. Before we make the trade official, I’d like to swap one side and drop in the cover rail to make sure it sits properly. 99% sure that the problem is the caps but I want to make sure it’s not an issue with the cover being made improperly.
I bought the steel caps from someone on this site that fabricated them. They look great and I wish the worked with the cover so I could keep the look but that doesn’t look like it’s happening.