5/3/1 5x5 is on page 21 of Beyond. Just do that.
Assistance work has not changed since the first book. Choose one (for the first two cycles or one if you are doing the 6 weeks progression) per session from the Wendler 6 (look it up). So, that is 4 assistance per week.
If you have enough energy to do 3 or 4 assistance work per work out, then your TM is way to low. After your 5x5, you want to go home. You just happen to stay for the assistance round, because you want to be better then your former self.
Don't forget conditioning. Hills are meant to ben run up.
And again, look up the 5/3 progression.
5/3/1 BBB 5x10 for two cycles
5/3/1 FSL for two cycles
5/3/1 go nuts for one cycle.
Go back three
Rinse and repeat.
Now stop whining and go lift.