Your temp was a little low but its within guidelines so you will have passed. Next time if the temp in the collection cup is a little on the low side, rub your thumb against your clothes for a few seconds and then hold it against the temp strip on the collection cup. When it says 98 walk out of the room.

They add blue dye to the toilet so you can't cheat by dilluting your sample with some of the water. No they don't test toilet water.
It depends on who the UA is for whether they split the sample. For most jobs a single vial is all thats needed.
Congrats on your new intern job.