Whether it's an operating loss or the sec 179 deduction, they will be disallowed and carried forward until the owner has basis.
If not taking the sec 179 deduction, does the S corp have ordinary income in excess of $3K? With a starting basis of -0-, that is the only way those excess distributions of $3K could be nontaxable because of the ordering rules.
I don't like the idea of switching the distributions to being due from shareholder, although it's a common practice. What do the books and records of the company reflect the transacton to be? If its a distribution, report it as such. If the owner had the intention to repay it, is that documented with a promissory note or in minutes of a meeting, or anywhere?
Finally, to answer the easiest of the questions you asked, if the stock of the S corp has been held more than one year, and if we are only talking about stock basis (no debt basis), then the excess distributions would be long-term.