I had a few engine comebacks over the years and what I did was eat the labor on the re-do and only charge the actual cost of the parts to me . the customers seemed to appreciate this , I also broke in the engine my self the second time and would use the vehicle for a few days to chase parts just to be certain .
In all honesty one or two of the failures were our fault , once I hired this " engine builder " and he screwed up two engines before I fired his [censored] .
I feel for you and hope you get it sorted out .