Too short a chain?
 

So, I tried putting a new Ultegra 9 speed chain while reassembling my bike after arriving in South Korea. I noticed that the connector pin was missing, though. So I took it to the LBS which speaks not a lick of English. It was very hard communicating with them. Anyways, the mechanic didn't listen to what I wanted and took 2 links off and then connected the links with another pin. The chain was positioned on my middle 36t and my rear granny gear 25t. I'm worried that the chain will be too short for a 48/15. I really wish the LBS spoke at least some English to explain what they were doing and why. Should it be okay? :(

Hard to say without a picture. Buy yourself a chain tool and take matters into your own hands!

Pick up therear wheel and turn the crank by hand while VERY CAREFULLY trying to shift into the 48/25 combination. Stop if you feel any real resistance. If it goes in, you are OK, if not, your mechanic screwed up and you will either need a new chain or be very, very conscientious to avoid that gera combination

You could downshift to increasingly larger cogs and check chain tension at each step.
IF it's too tight at 21 or 23, there's no sense going to 25!

Use a couple tiny screwdrivers or equivalent (nails?).
At each step, "hook" the nails into the chain (several links apart) and pull them together firmly, noting the amount of slack.

It's almost certainly OK for the 48/15 combo, but that's the wrong question. The chain needs to be long enough to loop the 48/25 combination, with about 1" to spare for the derailleur. Even if you never plan to ride crossed over, your chain needs to be long enough to do so in case you accidentally shift into it. The consequences of shifting into a combination the chain can't loop are too drastic to allow the possibility. They include a bent axle, broken dropout, bent chainrings, and destroyed RD, or any combination of the four.

Test as Hillrider suggested, but at each step pull the lower loop forward to confirm that there's extra length available for the next step.

okay, got it. Thanks. Today I'm going to Seoul where I hope to find a bilingual LBS to help me out. (I also need to repair or replace my crank set. The 48t got destroyed during the flight. I know I could just replace the single ring but at the exorbitant prices they charge here, I might be better of ordering online and swallowing the customs tariff fee)

I assumed he meant the 48/25 gear combination and the "15" was just a typo.

If you're in the right part of town Phil Shop can help you.

The owner Phil speaks (or at least writes) excellent English. I don't ant to publish his email, so I'll PM it to you.