I doubt CAT will swap you out with what has been written so far, maybe if the pump thing goes completely sideways that would help. Unfortunately sometimes regardless of how much you pay, and who makes it, things happen and the product isn't what the buyer or the OEM had hoped it would be. Clearly the machine wasn't right when it left the factory and perhaps the PDI wasn't thorough enough to catch some of that. This is/was an opportunity for the dealer to make themselves look very good, and done right you likely would never buy from anywhere else again (because in a shitty situation they had your back). Doesn't sound like they are taking advantage of that chance to prove themselves. Too bad for everyone.
Couple things I would try and negotiate:
Swap the machine out: Sure, why not try, kudos if that can happen but I think you will need a longer laundry list to see that through.
More realistically, I would make Cat or the dealer back your machine with a substantial bumper to bucket warranty. Zero deductible, and a loaner machine of equal size while repairs are made. Depending on how hard you want to drive the deal, the pickups and drop offs take time and money from you, I would consider that asstax as well, and decide what its worth.
If there are other machines in a similar situation, CAT may have a problem with production of these new machines. Now days an OEM cant keep those things a secret. Maybe they will do something for all those who bought these early production machines and are having problems. History would say they wont, but who knows.
The last thing I would say is $110K for a 299D3 seems like an awful lot of money. I totally see why your pissed, hopefully your dealer does as well.