Is 3900 hp OK for that CR?
I'd say so. Most of my abominations only have around 3-4,000 hp and they're CR 70+, but they have better defenses that Cloverfield here.
Off the top of my head, a 50th level fighter has a...let's see, roughly +100 to hit, give or take (assuming 50 STR and a +20 weapon).
So, on a Dire Charge, with Uncanny Power Attack and Leap Attack, he gets a full attack at +100/+95/90/85 Power Attacking at a 6:1 ratio (let's assume a greatsword).
Now, I don't think it's unreasonable for him to have an approriately dense weapon, so his base damage, at a guess, could be something like: 6d6 +60 15-20/x4.
Now, with Clover's horrendous AC, he's getting a full PA in on almost every hit, which translates to a +300 damage on each hit, bringing us up to 6d6 +360 damage.
Now, one of those attacks is likely to be a critical, which hits for 24d6 +1,200.
Leaving 3 attacks at 6d6+300.
Therefore, on average, our fighter deals Clover a rough average of 2,400 damage per round.
Now, to be fair, that is optimized a
bit. (I call it focused) However, it could go a lot higher
very easily. And the build is fairly obvious when you have feats to burn. There's only so many epic fighter feats of use, why WOULDN'T they take the Power Attack and Critical line? So I assmume this is a fairly stereotypical build for this level.
So...Clover lives through the first round most likely, but the fighter's buddies are likely to finish it off before it gets a turn.
If we could just get his AC to like 70 or so, I think Clover would be in pretty good shape. (Of course, a caster would likely tear it apart in one round easily, that's just a failing of this type of monster, really. Not much you can do about it while it's still "Cloverfield". If it can't stand up to a typical 50th level party without giving it abilites that don't mesh with it's flavor...maybe we should bump it down until it comes out even.)