and the brand new 100% flat pads have to fit to the "waves" at the (used) disc´s surfaces first.
even if these "waves" are only very small the pads touch their "hills" only.
no wonder that you got a worse brake for the moment
drive a bit with braking and releasing and braking and releasing again and so on.
but pay attention not to overheat the pads and discs by that.
I suppose after 10-12 brakings the "wave" effect is gone and your brakes will work fine.
and no matter what kind of pads you use - mineralic / sintered / race(?) - the wave effect "works" everywhere.
but please keep an eye on thickness of the disks.
the original older one, like those from 1999-2007 busa, get very quick very thin when using sintered / race(?)
so i personally only use the (EBC) organics at my ´00 busa. good braking and longer lasting discs (up to 60-70,000 km)
and if the brake still feels squishy,
take the calipers completely off and apart .
remove all pistons, and clean the grooves in the saddles as well as the pistons and their rubber sealing rings meticulously.
the "old" Tokico - calipers definitely need this deep cleaning every 30-35000 km - my experience with dozens of gen1 calipers.
how to disassemble the calipers is very well described in the manual.
but :
sometimes the pistons are so tight in the calipers that you can only push them out with hydraulic support.
after that deep cleaning and with never more the wave effect (pads/disk) you will have again brakes
even you "only" use the organics.
other reason for squishyness:
steel braided hoses mounted already? no? do it. the rubber hoses "pump" after some 10 years and you loose a bit of pressure ==> squishy brakes.
but pls never forgett - even at my fabulous working brakes i can pull the lever with big hand power completely to the throttle grip - when the bike STANDS - never when rolling !
this is usual / normal - i had a 30 minute phone call to brembo germany engineer and he fully confirmed this way of working.
the lever´s way to throttle grip increases the pressure inside system and by that the force to the pads.
so you must still have a kind of a seemingly bit squishy feeling,
even after deep cleaning, steel braides hoses and perfect bleeding.