1) How long can someone plausibly get away with this kind of activity before arousing suspicion and/or getting caught?Yes, it's called bail. Look it up.
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?
A writer is also a researcher. You should be able to find that out by looking up your criminal laws.3) What would be the official charge against someone engaging in this type of crime?
That's also something easily researched.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?
Those are things every writer has to figure out for himself.5) What are some of the potential issues/problems with this storyline that I haven't foreseen?
I'm sure there are plenty of novels out there about embezzlement that will give you some ideas as to what excites a reader.

