A co-worker needs a need chain for his bike. Unfortunately he had a problem a couple of months ago on the way to work and someone helped him with the problem but this required them to remove some links in his chain. He doesn't know how many links they took out, but he indicated that he has the odd problem with the bike that he believes is caused by the chain being too short.

By now his chain is worn enough that it should be preventively replaced. He asked me to assist him, but I'm not sure how long to make the new chain. Normally one just matches up the new with the old and makes it the same size. In this case we know that won't work. Should I simply match them and make the new one about 2 or 3 links longer?

There't probably any number of threads about chain length sizing - but general rule of thumb is loop around biggest front + biggest rear, bypassing the rear derailer. Then hook the chain up by the next longer available link.

+1 Above info is correct. Search Sheldonbrown.com for details.

Your friend will need a chain tool to cut the new chain to length. I would also suggest that he get a chain with a "master link" for joining it; I find the Shimano "special joining pin" concept to be flawed. SRAM, KMC and Wippermann offer chains with the connecting link included.

If the chain is significantly worn a new one may not play well with a similarly-worn cassette/freewheel, which may also need to be replaced. If the chain does not skip then it will be fine, otherwise replace it. Your friend should be prepared for this possibility