Chain replacement - how many links 114/116? I'm replacing an (exact same) Shimano 11 speed chain, the cassette is Shimano Ultegra 11-25T . There are 54 links that look like ()().  What size of chain should I order : 114 or 116 ?

I'm going to take the old chain off and then use the method 

thread the chain onto the large/large combination, without running it through the rear derailer. Mesh the two ends on to the large chainwheel so that one complete link (one inch, -- one inner and one outer half-link) overlaps.
It doesn't really matter -- either way, you'll be shortening the chain (this is true for almost any regular bicycle drivetrain). So I'd order whichever is cheaper; You can't really splice 11 speed links back into a 11 speed chain reliably, so having spare links on hand doesn't justify buying the longer chain. 

The easiest way to size the chain is simply to count links and match it with the oldchain. Then, break it appropriately and install on the bike. You can do this by putting both of the chains on a piece of newspaper, then pinching the links together to count them. But if you're changing chainring/cassette sizes, you may want to use the largest cog+chainring method (see also this link which also presents a simple formula if you want to just measure the chain with a tape measure).