Like I said above, the bike fit is most likely a fair way out (sounds like the saddle was already too low if the OP was able to ride with their mid foot on the pedal), suddenly changing from mid-foot spazz cycling to ball of foot would require the saddle to go up some way (several cm) if this isn't done then the new riding position will engage muscles differently, even with a non-economic pedal stroke. If you don't put it up you will be cycling with your heels down (would explain calf's aching) or cycling like a T-Rex walks, i.e. with constantly very bent legs (that would make both your calves and your thighs ache). For a very simple sanity check on this theory you could lower your saddle a cm or 2 and cycle for an hour, noticing where you feel you are deriving your power from, then try going the opposite way. A few cm difference in saddle height really can make a hell of a difference as to which muscles are emphasised.
IMO, and this strictly opinion, I think the fit is more the culprit than the ability to pull up on the pedals.
Would be great if the OP can confirm the fit and any alterations made etc, then I can STFU.