Is this for real?

I booked a bargin round-trip economy class ticket Kansas City to MNL through Vayama.com which includes NRT-MNL on Japan Airlines. I called JAL to make sure miles go into my JAL bank and politely asked if I could use my accumulated miles to upgrade to business on this flight. Guy said no as is not eligible booking class to use miles to upgrade. Mentioned that upgrade at gate might be reasonable in cost as business looked pretty empty on that flight. Friendly young guy and we got off topic chatting about petite Asian women for a minute or two. In closing, he said to check the website and my e-ticket.

A couple weeks later, I do check it and I am shocked as it now it reads that I am booked in First Class for that five hour flight. Can a customer service help dude really do that? Am I paranoid to think that once I get to the gate this will be caught and I will end up standing there several minutes looking like a douche bag while a couple supervisors ponder things and send my ass to the back of the plane?

Why would a customer look like a douche because of a mistake made by the airline? Just go for it, you stand to lose nothing. I am sure no one will raise an eye brow...

All, usually when you are upgraded the agent (telephone res, airport check-in, departure gate, etc.) usually has to specify in the computer how the upgrade is going to be "suppported" (or paid for).. In some cases it's an operational upgrade (airline oversold the economy cabin so they upgrade for free a few select passengers to the empty business class seats) in other cases it's a stand-by upgrade where the passenger has to surrender either a paper certificate or has to have the equivalent upgrade in his/her electronic upgrade bank with the airline..
When a passenger checks in and is doing a unsupported upgrade the computer normally triggers the agent to ask what form of upgrade the passenger will use to "support" the upgrade unless it was designated as a courtesy earlier..
And yes, agents can do these types of things.. I would note that the airlines have VERY good programs that watch what every agent does and will trigger a supervisor to questuion any transactions where it appears that rules have been broken, favors given, or other suspicious activity takes place.