Before I get too far in, I think it's worth noting that basically the only skills that specifically reference using skill rank bonuses are from the original Character Law. (There are a couple introduced in Arms Companion, but that's it.) Quite a few skills use the number of skill ranks in their resolution, but not the skill rank bonuses.
The three original skills are Runes, Adrenal Moves, and Adrenal Defense. Of these, Adrenal Defense is pretty much a non-issue because it explicitly states that there is no stat associated with the skill. Adrenal Moves we already know about, but Runes is another oddity; one that could have an impact on my ideas about Adrenal Moves.
In Character Law (1982) §5.842, Runes is defined to be resolved by making an open-ended roll, adding the "skill bonus," and including modifications from table 15.34 (Runes and Staves-Wands Table). This table repeats those instructions as a formula, specifically mentioning "skill bonus." Both of these mentions should imply using the full skill bonus with Empathy (and Intuition) as the assigned stat.
In Character Law (1985) §3.7, Runes is redefined to use the "skill rank bonus" in the full skill description, but table 15.34 still mentions "skill bonus." This change carries through to RMC2 (1987) and ChL (1989). In this case, since Runes is a regular magic skill with no delayed or transferred effects (a la Adrenal Moves), if Empathy (and Intuition, and profession bonus, for that matter) are still to be used as described, then it could clearly be seen as a mistake for it to have been changed to "skill rank bonus" from "skill bonus." The fact remains, however, that the description was never changed through two further opportunities to do so. One could have the position that, like filling out a blank check, if there's a question between what was meant, the part that takes the most words to explain takes precedence (e.g., the full, spelled-out dollar amount instead of the numerical amount of the check). In this case, that would mean the full paragraph description would outweigh the small, simple chart reference. However, I'm of the opinion that there's no reason why Runes should be limited to only using skill rank bonus, again, since it's just a straightforward skill with no special effects, and that ChL (1982) was correct all along.
Extending this logic to solving the question of whether to include stat (and profession) bonuses with Adrenal Moves depends, for me, on which Adrenal Move we're talking about. I can see Strength and Speed easily using Pr(/SD) instead of just the skill rank bonus because the rules as written clearly explain a successful roll of the Adrenal Move must be made before any effects are manifested. However, if the original intent WAS just to have the skill rank bonus apply to a successful roll attempt, then two other options surface. First, if Pr(/SD) are truly applicable, then a second, separate roll including them must be made, whose placement is not defined in the sequence of the preparation round/rules-as-written roll/effect round. This would be fairly unique, where two rolls of the same skill must be made for a full resolution (a.k.a. Double-Dipping). It would also be fairly cumbersome and seems unlikely to be unmentioned as such a departure from the normal skill resolution process. The second option is that Pr(/SD) shouldn't really be applicable, but that also seems unlikely because so much effort was made to mention the primary skill (twice, in the description and table 15.14) and a secondary option (+SD).
Since both of those options seem unlikely to be intended, where does that leave us with Adrenal Speed and Strength? I think it's reasonable to assume that stat bonuses should apply to their rolls, but this paints a darker picture for the accuracy of proofreading and copyediting on the original team's part. It would mean that the 1982 description should not have said "skill level bonus" to begin with, the 1985 description should have been changed to "skill bonus" instead of "skill rank bonus," and that the 1987 and 1989 descriptions were further missed for an opportunity at correction -- almost a fractal-level of wrongness.
Now, for Balance and Leaping, the question shifts away from how to make a roll for the skills, themselves, and toward how they are applied to other separate maneuvers. In this case, assuming that only one roll in total is needed to determine success, that roll would necessarily be the secondary maneuver skill made after the preparation round. Otherwise, the same scenario as above of two options being possible comes into play. However, each of these skills has one additional factor that argues against using a second roll. For Balance, the Runes scenario applies, where the original ChL (1982) description said "skill bonus" and later versions all said "skill rank bonus," thus originally implying that the Pr(/SD) bonus would be included in the following balance maneuver. For Leaping, the description says that the (whichever edition you choose) bonus is automatically applied to the leaping maneuver, thus implying that there is no roll at all for the Adrenal Leaping skill, itself.
Finally, the description for Landing states that it automatically reduces the level of the fall, again implying, as with Leaping, that there is no roll at all for the Landing skill, itself. The question, then, for all three of Balance, Leaping, and Landing, actually, is how much bonus was intended to impact either a secondary skill's success or a direct physical effect (either the full Adrenal skill bonus or just the rank bonus). We do know that people did review the skill descriptions over time because ChL (1989) changed Landing from a moving maneuver to a special skill, so the possibility existed that they could have clarified/corrected the other skills, too. I would have no problem using the full skill bonus for these three skills, but that would be a playtesting issue, of which I am no authority to decide.