Bicycle Mechanics - New chain roughness

I recently bought a new transmission with an 9-speed Ultegra cassette and Ultegra hyperglide chain. I stupidly cut it too short (the air was blue) and had to break it in a different place and add some more links with the result it has three replacement pins in it.

Not the best situation but I figured I'd just have to replace it when I break it to give the whole thing an overhaul in a year's time or so, but...

When I push hard from lights, up hills etc I heard sporadic loud clicks and felt a slight jump in tension which I narrowed down to the replacement pins going over the chain ring (even the first one which should be no different than if I got it right in the first place). I took a look and thought maybe I pushed the pins too far so pushed them back a little with my chain tool.

This got rid of the clicking but now there's a roughness in it, again pins going over the chainrings. I've checked that none of the links are stiff. I'm guessing my chain is now screwed and I'm going to have to plump for a new one, but any thoughts to the contrary or any advice for when I put another on?

I've broken chains a few times before (intentionally with a chain tool for overhaul) and never had these problems, but inevitably it's not something you do often (unless a mechanic) and nuances of what you did get forgotten.

I'm not certain what the ultimate answer might be, but I'd ask my LBS for advice and probably be prepared to spring for a new chain.

Ahh, have you made sure the links aren't stiff? Where you put the replacement pin, you have to grabe the chain (preferably in a rag) and flex it back and forth. The insures that the side plates aren't pressing too hard against the inner plates.

Yeah, this sounds like a stiff link(s) problem to me. You don't need to replace the chain but you do need to loosen those links up to be flexible. Stiff links can be a serious problem if the chain doesn't run through the rear derailleur smoothly. If a stiff link gets stuck in the derailleur it can be fatal to the derailleur and even the rear triangle of the bike's frame. I've seen it happen.

Al

Pedal the bike backwards and see if the rear derailer jumps at the stiff link. When a botom bracket fails / is failing it makes an occasional thunk/click. To check that take the chain off of the front chainwheels and see if it spins well. Sometimes you have to pull the crank arms and spin the spindle by hand to feel if it is tight, since the crank weight can fool you into thinking that it is smooth.

The BB is brand-spanking new too, and a cartridge type 105 one, so I'd very much doubt that is the cause.

The links were stiff after I adjusted them previously to remove the click which I remedied with the chain tool. Since then I've watched the chain as it goes through the rear mech, flexed the links etc and I've been unable to see any stiffness. I'll give it another go when I get back from work today.

Otherwise it's off to the LBS I guess, unfortunately the shop I bought the parts from was closing down (a 25% discount prompted me to finally sort out a new transmission!) so I can't rely on their usual after-sales advice - will have to head to another and cough up.