Let's see that there are many errors within this discussion

1 zilla, godzilla 99 and zilla JR are separate entities.

one of the biggest mistakes I've seen around here is a common mistake about these 3 totally different entities what happens is that godzilla 99 is the famous bad american movie which was later satirized in one of godzilla's last classic movies where the japanese demoted it as zilla

after that the release of the animated series trouce a new "godzilla" more faithful to the original and this one did justice to the name (if you doubt just watch the series)

the big problem is that by then fanbase no longer saw zilla and godzilla 99 as separate entities and only by hate and satira they nicknamed it zilla as if they were both the same entity

and soon after creating the nickname Zilla JR for the godzilla of the series (which is never called during the entire series of just Big G, G mam or godzilla JR)

let's go to the facts

godzilla 99 and zilla JR would have no chance against ghidorah since no equer are considered godzillas by the community

zilla JR on the other hand wouldn't be able to hold a fight either but if his monstervese counterpart were exactly the same as the series i would say he would be a few levels above kong (since he is as or as strong as the monkey is capable to regenerate breathing in the water digging tunnels beyond his speed and intelligence are much higher than kong he also has an underestimated but extremely powerful atomic breath)