Good breakdown KP.
1) I like the story with Gotenks being a bit stronger than Goku. I don't see an issue with that. I don't like the strength of Base Gotenks. Based on the reactions, he has to at least be stronger than the Super Saiyan boy's power. That puts on a lot of stress of the power leveler to ramp up the difference between Super Saiyan boys and Super Saiyan 3 Goku by a shit ton. I would be fine with Base Gotenks being a weakling by comparison. I don't think he needs to be strong if we intend on keeping the 50x boost here.
2) Post Base Power, this thing is fucked, he should be nowhere near his Super Saiyan self, which has multiple statements suggested he is, no matter how much stronger he gets, he needs to have the boys get a lot stronger as well. And for Base > Post, no matter how small the multiplier, it's impossible. Goten and Trunks are not stronger than their dads now.
3) Gohan is an easy fix imo. If you fix the art make him a Super Saiyan 2, there are only two issues that I can think of.
His statement about Initial Fat Buu, probably needs tweaking. I rather have Buu weaker than Dabura and Gohan, explaining Dabura's confidence and Gohan's attitude as well as Vegeta's mockery. The second issue, I would tweak how Gohan speaks about Goku's damage power, he speaks as if it's on another level.
Besides those two statements and of course the art, there is literally nothing else that suggests Gohan is a Super Saiyan. Which is why I feel Gohan being a Super Saiyan 2 is best for the story. It also allows you to have Gohan >>> Kaioshin >> Piccolo, which is how it should be imo. Also let's South Kaioshin be Perfect Cell level, which is entirely respectable for the strongest God.
Ah, you also have to change Majin Vegeta into a Super Saiyan 2 from the getgo. We can't portray Super Saiyan Majin Vegeta as the beast he is. Also, Kaioshin getting shitted on by Super Saiyan Goku needs to get changed into Super Saiyan 2. I think those are some minor changes honestly, but others might not agree.
I have no issues with Gohan's power ups throughout the saga, they are deeply tied to his dormant potential, so no issues in my book.
I have answers for the Buu situation. I think there needs to be a statement that says after Fat is ejected from Kid, he regains his former power. Then after that, all problems fixed in my book.