Simple snake noob questions

[Craiga 01453]

Welcome to the forum.

Based on your questions I'm guessing you didn't do much (if any) research BEFORE bringing the animal home. Since you were googling what substrate to use while in the store you clearly have a LOT to learn.

Start here:
pythons.net/forums/showthread.php?127203-Ball-Python-(Python-regius)-Caresheet

...and here:
pythons.net/forums/showthread.php?31102-Ball-Python-FAQs

Now on to your questions:

1) YES, feed in the enclosure. Eating a little substrate won't hurt the animal.
You've "Come to realize" you have aspen bedding...and you're concerned your snake will get sick because another snake got sick from the substrate??? You sure the other snake wasn't on pine or cedar? Both can make snakes sick...

2) YES you need a vet that sees exotics, and hopefully is well educated on snakes specifically. Most vets are not very well educated on snakes and only know the tiny bit they had to learn to pass their required courses.

3) Yes, the snake will probably eat the mouse. Yes, you can feed it to the snake, but you run the risk of the snake refusing rats moving forward.

4) snakes can not "smell fear" but they are very receptive of fear. They pick up on advanced heart rates, shaky hands, twitchy movements, etc...and will often become nervous themselves because of it.

Follow up from your comment above: your snake is NOT lifting it's sides for you to pick him up. Quite the opposite.
It's moving it's body away to tell you it doesn't like being touched or is a bit nervous. They don't want to be picked up. They TOLERATE handling but would MUCH rather be left alone.
Since you've only had the snake a week, you shouldn't be handling it yet anyhow. Let the snake acclimate to its new surroundings, new smells, environment, etc...
I strongly advise, new keepers especially, to let their snake settle in and start eating regularly before handling. The snake getting acclimated and eating is most important, you'll have 20 years or more to handle the snake, let it be til it's got three consecutive meals without refusal in him.

Do yourself AND your snake a favor and start doing some research on the living, breathing animal you brought home.