i think your gym program is okey..since your WO just for 2 day..split program (upper n lower) is acceptable..
try to focus what you what first..get stronger or more endurance? dont been greed to get both..its just like your drive a car n want to turn right n left at the same time..well its not totally impossible, but its hard
form my observation on your regime..i think endurance if fitter for you..(cycle for 40km, running ect)
you dont need calf raise...running n cyclling already help you raise them..try to limited leg wo..but give some attention on mobility more
my suggestion is
wo a:
OHP
BP
dip
pull up

wo b
DL
SQ
abs (abs roller is the best,plank)
back extension
some mobality work..