UTR, it seems we are in agreement anyway... lets see if I can formulate the points we both agree on:
The platform may have been able to perform self-escorted strike missions, but at too high a cost per flight hour - Correct?
"Too" high is determined by the bill payer. I will agree that it was higher than a Super Hornet.
Kosovo was not a high-threat environment (too little modern mid/high Alt missiles, no serious networking between ground defenses) and the F-117 was lost more to being stupid than anything else (same ingress route on multiple sorties...)
Kosovo was as fearsome an environment as we have faced so far. For me the only real threat out there that is still an unknown is the SA-10. As far I as I know, none of those has been fired at any US Warplane. Even the vaunted Strike Eagle is gonna need SEAD support going against an SA-10 site. The Super Hornet and F-16s can protect themselves with HARMs but will the F-16 be able to do anything else?
As far as replacing the D Cockpit, at least in the European market I'm very aware of an ever growing problem to maintain clockshop pits due to the lack of knowledge and spare parts. The people who built these things are retiring quickly, and the number of technicians in avionic shops who can handle those delicate instruments is falling just as quickly. A lot of glass pits are rolled out in EU Forces just to get rid of the maintainance requirements inherent in old-style cockpits.
Nice bit of glass in that pit. In America, we have planes that are older... a lot older... than the techs that service them... look at the B-52. Not a problem for us.
And while the radar was not bad, it certainly would not be state of the art today. Adequate for low-threat conflicts like currently ongoing, but less than optimal for high-threat work.
No. I see no reason to believe the APG-71 was lacking in any vital function. Ground mapping radar modes are not as vital to effectiveness like they were in the 80s. GPS is king. The Tomcat has an app for that!

I would formulate my point such that a Super Hornet - quite logically - can perform deep strike missions much safer (modern self-defense, materials, RCS...), and for less cost per hour than the Tomcat could have.
The most moder self defense systems are modular and adaptable.
http://iews.es.itt.com/sp.aspSome of these systems are deployed on multiple platforms. The AF has systems that are installed in both the B-1 and the F-16. With its modern data bus, there is no reason the later versions of the Tomcat could not be adapted to carry the latest offerings in self defense. Again, we are not gonna see SU-33s and SA-10s all over the world and where we do encounter them, dedicated SEAD assets will almost always be required, regardless of strike platform.
Of course you can modify almost any aircraft for a new role - as they started doing with the D - but if airframe life is also an issue, it obviously was simple cheaper to buy new jets.
This is not really within the realm of the original point I am arguing but, there are several platforms in the US inventory that have this issue. You make it if you need to. The Navy had options and made their decision. The AF on the other hand, with only 120 F-22s is gonna have to figure out how to maintain air supremacy with F-15s literally falling out of the sky because they are so old. The Navy did not lose any Tomcats to structural stress, that I am aware of. Look at the A-10s.
That's what I was saying - I wasn't questioning the ability of the "Bombcat" to do today what Hornets are doing today,
Does not square with "And the Tomcat really was good only for one thing"
As for my original statement where I said "it would have required massive changes to become a true multirole platform" - I'll qualify that to explain that for me True Multirole means survivability in a current day high threat environment. Simple being able to drop a few laser guided bombs on a camel trail would do for today, but not for tomorrow, and this additional cabability to remain "safe" would have cost a pretty coin.
We are close enough for gov't work here. Currently, I see the Super Hornet as the only jet in the US inventory that clearly has a better chance by itself in your scenario. I don't think the Tomcat D was that far away from the Strike Eagle with a few systems upgrades. The Super Hornet has the latest defensive suite, the legs, the ability to carry the HARM and enough hard points for both ground and air munitions.
The question is, would a single jet ever get the mission you described? Fight SAMs and interceptors on your way in, kill a target and fight your way out again.
Sounds more like a video game than any real world tasking.
I believe a Tomcat D with a few upgrades, nothing massive, is perfectly survivable and effective given the threats we will probably face. There are certainly less capable aircraft in the inventory. However, the Navy had options and I think they chose wisely. or at least, did not make a completely retarded decision in going with the Super Hornet.