This is a repost sort of from a post I made on reddit a couple weeks prior. 2 ish weeks ago, I had redone timing chain guides on my 2005 MCS 6 speed (facelift) (86k miles if that matters), etc all went well, after starting up (went fine). I shut off the car from paranoia (should have let it idle), then after started again, car had super rough idle when trying to move to cold start rev range, nearly died and I shut it off after hearing a concerning chain ‘clang’ noise.

I recently opened the valve cover back up to inspect it, and none of the copper links line up like they did when installed, JUST like when I did it the FIRST time around (picture attached of most recent timing). I rotated the engine numerous times to no avail, it was one link away from the copper lining up but never did.

Although I have comments/questions:

• the engine spun just fine to me, I could rotate it 90 degrees and then it would then rotate around itself; this is normal yes? If it can do this, then the timing should be fine right?!
  
• Originally when doing the TCG, the links were NOT aligned yet the engine ran fine before I worked on it, this is normal then? I do understand they’re not supposed to always line up with each rotation.
  
• When I heard the 'clang' noise as the engine misfired, could this have lead to the chain skipping? This is my main concern now before I try and start it again, worried a valve may hit a piston, etc.

So, with this I should be able to just put it back together and go from there yes? Or am I missing something crucial.