If you want the manual over the CVT, I would first make sure I found that. For me, that would be the most important aspect of owning the car. I would also do whatever you had to to get the exact color/trim that you want.
Personally, I wanted a black manual base model. If I had had the extra couple $1000 to get the EX, in hindsight, I might have preferred that (mostly for the pre-installed sub that is probably placed better and more efficiently out of the way than any after market sub I could add and for little touches like the blue LEDs in the footwells).
I bought mine at a dealership 3.5 hours away because they had the exact trim/color I wanted and because I got an online deal for $1000 less than my local dealership that did not have the car I wanted, anyway. It also happened to be in the town my girlfriend's parents live in and I was there for Christmas, anyway. It will be somewhat of a pain if I want to take advantage of their free dent repair policy, but we visit her folks enough that that shouldn't be a huge inconvenience. For everything else, I'll just take it to my local dealership or shop. A Honda dealership anywhere should be able to handle a Honda under warranty.
In the end, though, have you asked the local dealerships that offered you a good price if they could get the car you wanted as a dealer trade or something? Maybe they would honor the price...I'm not really sure how that works.