Kyogre Question...

95%. You have 1 less attack but it survives attacks slightly better, but at the end there is no difference.

Your best course is to power up the 95% now, and work on getting resources to power up the other one. Also depends on moveset, if one has water moves already, power that up first, especially if you don't have a ton of CTMs.

But in the end, they are both great, and should both be powered up eventually. The differences between them are negligible.

No significant difference between the two; the 93% you do slightly more damage. The 95% you take slightly less damage. Over the course of a battle, it's probably getting 1 extra Fast Move off before fainting and for the 93%, for the 95% it's soaking 1 extra Fast Move before fainting.

I'd say that if you are able to dodge 1-2 Fast Moves in a battle, go for the 93% and do that little bit of extra damage.

(also, I'd take into account the Charged Move that the Kyogres have; if they're different moves, I'd probably prioritize a Blizzard Kyogre over a Hydropump or Thunder due to Rayquaza being out now.)

I would not be surprised if after breakpoints they were functionally the same.

So here is another comparison:

14h/15a/13d
Lv 30: 3470 cp
Lv 35: 3759 cp
Lv 40: 4049 cp

15h/14a/15d
Lv 30: 3471 cp
Lv 35: 3760 cp
Lv 40: 4050 cp

So if you care at all about the numerology of your pokemon CP, you have an interesting situation: 4050 is a round even number (5x5x3x3x3x3x2) while 4049 is a prime number. Is either of those something that you would care about?