What type of end caps? The SR5's came with no flares, chrome flare strips, black textured flares or limited type flares. The first three use the same end caps and might not work with BW's. The limited type flares most likely will work fine with the BW's. I'm sure you can swap the DS rear end cap to the PS front end cap location and the PS rear to the DS front. I'm not positive, but it should work.
I have the bushwacker flares and I used the limited/sport edition running boards. For the rear end caps I left the sport edition end caps on the running boards and for the front end caps I used the rear end caps from the limited running boards, just switched rear left to front right and rear right to front left. That is the best way to get good flowing lines with the bushwacker flares and factory running boards. I had to buy two sets of running boards but it was cheaper than just buying the end caps from the dealer, they want over $100 for each end cap.