It looks like you're gonna have to get more people involved.
from what i understand:
1. you took your car in for clutch issues
2.they lost your keys in the process
3.they did not adequetly keep you informed of status
4. they changed their stance on coverage
5.they based their judgement on subjective opinions (ie

robable cause) on how you drive as cause of failure because there is no objective reason why it failed (no mech proof).
Im assuming you tried to get the dealer mgr & honda HQ involved. Do they know every dealer sells a/m pts like what they are accusing as to why the pt failed?Have you tried filing a claim w/your ins co? Some instances, they will cover mechanical failures. If not, that dealership will have what could be first of many 3rd party people coming in to inspect car. at least you will have an unbiased opinion on why it failed. you can at least file claim for the lost keys & alarm which the dealer is liable for. Ask the ins co's appraisers for his opinions & what resources he might have that you can use.
Im no lawyer but you have at least a bad faith lawsuit against them.
if all fails, neg pub always works. I was working at a LA dealer & some cheap&shrewd fvck contacted Mike Boguslawski (dude on ch. 2) for something totally bs. anyways, all dealers hate neg pub. our mgr said "just take care of it" meaning make it go away.
Ive worked at 2 very large dealerships & this is not a very large issue considering what can come about from this. Do they want to go thru neg pub & months of litigation re

ver $2k? They do this because they feel they can get away with this. If they felt you or your family had more clout , was well versed in legal matters, or was a more informed patron, they would not be so quik to deny your warranty. they obviously lied to you (at best, misinformed you) during that 1 wk where they did not work on the car to make sure they had enough backing to deny your warranty claim.
I would approach whomever has the rank there one last time for these questions & really read into his answers (or lack of). If his response is vague or if he goes off in a tangent or for any reasons they seem illogical or not satisfactory, you will know he himself has no valid reason why they will not cover damages.
At that point, dont scream lawsuit & threaten him of one. Just let him know that his answers were not satisfactory & make certain he understands your intentions of hiring council to at least get clear answers out of him & that he would be directly responsible to back up his dealers decisions in a court of law.