Not sure about the Cluch Pedal 'Clunk", but if it starts cold and fails hot, possibly the CPS is getting flakey.

Search CPS for additional details.

Typically a faulty CPS will allow a cold start, but kill engine once hot. Let it sit a little to kool, and it starts right up.

If the starting and Clutch noise are remotely related to your issue, then possibly not CPS related.

I'm not sure how a Clutch Clunk after starting could be associated with hard starts when warm, but nothing would surprise me lately...

And you need to pull the Codes...this will narrow your adventure...