Hope that helps you out. Well....you really shouldn't need to recalculate get hits since you can just use the values that I use. 
Yeah, I notice all characters uses the same air.velocity and fall.yvelocity value 
- Can anyone explain to me how do I use this formula to calculate the damage?: damage = floor(42*ifelse(var(56),1.25,1))
I tried to figure out for weeks and I still can't get it.
This one is pretty simple. If var(56) (counter hit check) is true, than the damaged will be multiplied by 1.25 (floor is used to round it down to an integer, since you can't use floats for damages). So 42*1.25 = 52.5 which is rounded down to 52
If var(56) = 0, than the damage will be multiplied by 1 giving the same value. 42*1 = 42
The calculation of damage value is weird, I am not sure did I use the damage calculation formula wrongly or something, this is how I calculated the damage by using weak close punch as an example:
from your Kyo:
;CLOSE A
[Statedef 200]
type = S
movetype= A
physics = S
velset = 0,0
ctrl = 0
anim = 200
poweradd= 0
sprpriority = 2
juggle =10
facep2 = 1
[State 200, snd]
type=playsnd
trigger1= animelem=1 && random<500
value=200,0
channel=0
[State 200, Punch Attempt Sound]
type = Playsnd
trigger1 = time = 0
value = 3+(var(32)*2),0
[State 205, 1]
type = HitDef
triggerall = var(40) < 1 || var(57) > 0 || var(16) > 0
trigger1 = AnimElemtime(2) >= 0 && animelemtime(3) < 0
[b]damage = floor(42*ifelse(var(56),1.25,1))[/b]
sparkno = s17000+(var(31)*10000)
sparkxy = -10, -80
hitsound = s3+(var(32)*2+((random%3)*var(32))),1
guardsound = s3+(var(32)*2), 12
guard.sparkno = s17500+(var(31)*10000)
attr = S, NA
animtype = Light
air.animtype = Back
ground.type = High
guardflag = MA
hitflag = MAF
priority = 6, Hit
pausetime = 7,9
guard.pausetime = 7,8
ground.slidetime = 9
ground.hittime = 8
guard.hittime = 8
guard.slidetime = 9
guard.ctrltime = 16
ground.velocity = -5.796875
air.velocity = -4.5,-7
air.juggle = 0
getpower = 47,47
givepower = 16,16
air.fall = 0
forcenofall = 1
ground.cornerpush.veloff = 0
guard.cornerpush.veloff = 0
air.cornerpush.veloff = 0
yaccel = .5
persistent = 0
[State 200, 7]
type = ChangeState
trigger1 = AnimTime = 0
value = 0
ctrl = 1
So 42 is the damage value and when I check using kof98's Kyo from the art money table, it show that the damage value is 99
so when I use the formula:
damagevalue / maxlife * 1000 = MUGEN damage value
99/103 * 1000 = 961 
or maybe if I take 103 - 99 (I assume 99 is the life gauge that is left) and the value which 103 subtract from 99 is 4 which is the damage value and this is how I calculate:
4/103 * 1000 = 39 and it is not 42? I am confuse 
this same goes for the power gauge, I managed to calculate all the basic attack's hitdef for getpower using Kyo from kof98's close weak punch as example:
Total kof98's powergauge is 128 so
6/128 * 1000 = 47 which is correct, but when calculating command attack and special moves, the calculation feels confusing and wrong such as I use Kyo from kof98's Weak 75 Shiki Kai (first hitdef) as example:
Your Kyo shows get.power is 16 but when I calculate, it shows
4/128*1000 = 31 and it is not 16. I am not sure did I calculate wrongly or using the formula wrongly?