I'm going to go for a split here. Neither has enough in terms of appearances to gauge who was the most powerful of the two. Just because RK Thor did not restore 97% of the multiverse does not mean that he could not, nor does it equate who is more powerful, when comparing these two powerhouses. Split.
Due to plot and storyline. This however does not mean that he was incapable of doing this. King thor was capable of massive matter manipulation, so I don't see why it would be outside of his power-set to take it up to the degree that CW Herc did if he had an amp in power (rune amp).
At any case, the safest answer is a split between the two, because of the lack of appearances, feats, and that RK Thor wasn't around to encounter a threat like CK (plot limited). I'm pretty sure that if RK Thor was placed in the Chaos Wars story arc instead of CW Herc, that his showing would have been just as great, and since he would be drawing from the runes, he may have even retained his power level, unlike Herc, who was drained from the feat.
You see the arguments that could be launched in support of either side? Well there simply isn't enough evidence to support either side, outside of perhaps one impression over the other. Split is the way to go here.
While I disagree with you, I think you're putting up a good argument. One thing I think RKT has over CW Herc is confidence level. RKT always seemed cool and in control, while Herc, while powerful, still seemed like a buffoon.
Even still, until we see evidence of Rune King Thor being powerful enough to deal with something like CK, we can't assume he could either.
Well i would have placed RK Thor far above Odin, and we all saw how well Odin did against Galactus. RK Thor may actually be on the level, but he simply did not have an opponent on the level of the Chaos King to show for it. This does not mean that he would have done worse than CW Herc. he may have actually did better. I for one believe that RK Thor would have beaten Galactus' ass or at least Galactus on the level that he was when he fought Odin.
The answer to this thread lies in the origin of each characters amplification. Was Herc's amp greater than Thor's amp? Now let's look into the why and why not.