Epic spell development is a mess, you can probably get away with improving multiple abilities with a single use of the base seed.
Your quoted text for the Fortify seed does state that you grant a bonus to "Any one ability score", and I would personally have been tempted to judge that this means you have to use the seed multiple times if you want to apply a different bonus. However, I figured I would look at the existing epic spells to try and figure out whether or not it's really the case that you need to double up on the base seeds in order to use multiple different effects from the same seed, and it seems like this is not consistent (sometimes not even in the same spell).
Case in point, the Origin Of Species: Achaierai epic spell. It uses the conjure, life and fortify seeds to create an entirely new creature and improve its abilities:
To Develop: 360,000 gp; 8 days; 14,400 XP. Seeds: conjure (DC 21), life (DC 27), fortify (DC 17). Factors: +4 HD (5 hp per HD) (+20 DC), +6 to natural AC (+12 DC), add three more natural attacks (ad hoc +6 DC), add black cloud spell-like ability (+33 DC), add SR 19 (+15 DC), permanent (×5 DC). Mitigating factors: ...
Here shown is that the fortify seed has its base DC of 17, but it adds both 4 HD (by adding 20hp, +20DC) and a +6 natural armour bonus (+12DC) - two different effects - without needing to double up on the seed. However, it then goes on to add SR19 for +15DC - which is actually derived by taking the fortify seed again with a base DC of 27 for the spell resistance version and reducing the granted SR by 6, which lowers the DC by 12 to arrive at DC 15. If a single use of the seed could have done all of these, the spell would be easier to cast.
Hellball is also notable:
To Develop: 810,000 gp; 17 days; 32,400 XP. Seed: energy (deals 10d6 each of acid, fire, electricity, sonic) (DC 76). Factors: double base area (+6 DC), 1-action casting time (+20 DC). Mitigating factors: 10d6 backlash (-10 DC), burn 200 XP (-2 DC).
It clearly uses the energy seed four times for the four different kinds of damage it deals - 4*19=76. If it was a single use of the seed buffed up by adding +30d6, it would actually have DC79.
But anyway, your spell
The Origin Of Species: Achaierai spell shows us a clear example of the fortify seed being used only once to grant more than one of its possible effects simply by increasing the DC appropriately (even if it goes on to actually double up on the seed for a different effect) so it seems legitimate to have one use of the seed affect multiple ability scores. Final adjudication on the spell you develop, however, will fall to your GM:
In all cases, the GM determines the actual Spellcraft DC of the new spell.
You're playing epic, so any pretence at balance is already long dead and buried; just do whatever your DM will let you get away with.