1) How long can someone plausibly get away with this kind of activity before arousing suspicion and/or getting caught?

Months, years. Depends on his position in the company, how smart he is, how often audits are done.

2) Is it plausible that someone could be facing these types of charges and still be able to remain within the community while awaiting indictment/trial?
Yes, it's called bail. Look it up.

3) What would be the official charge against someone engaging in this type of crime?
A writer is also a researcher. You should be able to find that out by looking up your criminal laws.

4) The protagonist will ultimately end up being convicted of the crime in this storyline and will go to jail. What I would like to know is how much jail time would he likely be facing?
That's also something easily researched.

5) What are some of the potential issues/problems with this storyline that I haven't foreseen?
Those are things every writer has to figure out for himself.

I'm sure there are plenty of novels out there about embezzlement that will give you some ideas as to what excites a reader.