Your most likely unable to buy valkyr prime chassis because
1 she is vaulted
2 if you can't easily get it, it is most likely the rarest part. Which is still obtainable if your willing to spend more plat than non vaulted frame would cost.
As for which prime you should pick. Most primes only have slight increases in stats. One of the Warframes which has a notable stat difference is atlas prime. So in this sense he is really worth it as his effective health is quite a bit higher from his normal varient.
Otherwise. Does it really matter? Some of the biggest differences come from having "prime" added to the name and getting a different skin. Oh and you get 250 energy from death orbs. Then there is usually a slight energy/speed/health/armor/shield upgrade.
Just build a prime when you have collected the parts and don't worry about it.