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I bet you look like a RAISIN when you get out!

J/K...in all seriousness...

How old is Rylee again?
I don't have a good answer for the poo...maybe instead of smaller like we usually say to keep the area, maybe he needs a bigger area if he knows to go on the pad, but then is stepping in it. He needs a separate area for pad/laying etc.
Is the play pen small enough to take it in the bathroom with you? Or put it where he can hear you and you can talk to him some to help calm him?
You are right about needing to get the separation anxiety out of him before you go back to school...you don't need to be worrying about him while you are in school.
I would suggest short trips and lots of praise when you come back in...let him know you will always come back. Closer to school starting you should wean him to staying alone that long if nobody will be with him during the day. He will eventually get used to the routine of different days.
Brink can tell the difference in work/school days, and weekends...and church nights and ball game nights...he usually knows when he is going and when to assume his perch on the back of the chair...Rylee will get it too...give him time...