Hi martin,
Okay, a few questions - what is the $525 covering under routine fluids, and why would that be the same for both vehicles? Newer vehicles usually throw in free oil changes for the first year, and even 10 years ago the sealed radiator systems only needed to be flushed maybe every 75k or 100k miles.
You throw in $250 for mechanical repairs on a new vehicle, but I would imagine that anything would be covered under warranty. Maybe this is budgeted to cover a flat tire or non-warranty work?
You also say this new vehicle gets 40MPG. That's rather impressive and I wonder if it has the same carrying capacity as your 97 Jeep. With the family, safety is a consideration and for me personally, 1 grand a year to have my family in a safer and more reliable vehicle is probably worth it.
You might want to consider a car that's 2 years old. Someone else has taken the depreciation hit, they are typically still under warranty and that can be extended, and most of the kinks are worked out.
I like your breakdown and only question the above because it might make a new care more attractive. You also list $2400 annual repair for the Jeep, and I'm curious to know if that's backed by historical fact? If so, I'm not ever buying a Jeep.

If that's because of your 3rd tranny, you need to go to another shop that knows what they are doing.

Maybe that $2400 needs to be spread out over more than one year for accuracy?
Something I'm running into on the same topic is tires. My truck is going to run me ~$750 for new ones. If your Jeep is running down on tread, you need to factor that in, as a new-2yr. old car can spread that cost out more.