I read it as: humans kidnapped, clones started, humans turned to histachii. Then the histachii were killed before the clones were born, avoiding the insanity clause.
Let's just go ahead with Powerful Build on all of them but not boost the Str as much on the Large ones as standard advancement suggests.
Not sure I like that, but let's work the numbers and see how it looks.
Obviously we want a Strength bonus, but the original's mediocre hit points suggest their Con isn't improved.
Indeed, going by the examples it might be penalized:
The 1st Gen Megamen have 10 hit points, which is 1 hp less than the 11 hp average for a 2nd level fighter.
The 2nd Gen Megamen have 20, 14 and 12 hp, which averages 14.66. That's 2 hp less than an average 3rd level fighter's 16.5 hp.
The 3rd level Megaman has 25, 23 hp, which averages 22. That's 2 hp
more than an average 4th level fighter.
That suggests the strain of the procedure might weaken their health, resulting in a Con penalty.
I also suspect they're pretty stupid, like the "near mindless" Histachii, which have -4 Int and -4 Cha according to their
Monsters of Faerun template. I'd use the same mental penalties for these big lugs.
How about:
1st Gen +4 Str, -2 Con, -4 Int, -4 Cha, Powerful Build
2nd Gen +6 or +8 Str, -4 Int, -4 Cha, +1 size category
3rd Gen +8 or +12 Str, +2 Con, -4 Int, -4 Cha, +1 size category
I'm not much fond of Powerful Build and a size increase.
A +12 Str non-elite warrior Megaman with a Huge greatclub could do 3d8+10 damage, which is more than the SRD Hill Giant. The original text lists their damage and it's significantly less than a Hill Giant.
I'm tempted to limit the Powerful Build to the 1st Gen version.