"what effect all the ergometer training will have on the 5/3/1 program" - it's not the program but the lifts that may have a problem with the extra lower back work. My advice would be to use a 2 day/week program (as shown before), use 85% TM, 5's PRO and figure out the FSL volume slowly.
Other than that, you are going to have to be smart. With any sport, it's a balancing act. The smartest thing to do is keep a written training log in a spiral notebook and make notes on what you've done/how you feel, sport performance, etc.