If I replace an attack value using the Batman Enemy TA could that value then be modified higher? Say I have Lady Shiva and Two-Faced standing right next to each other and Two-Face uses that Batman Enemy TA to increase his attack, would the attack value be increased higher if he had the loyalty token on him from the fast forces Penguin.

Yes. Rule: replace (bat enemy) and then modify (Perplex, penguin token, etc).

Reminder: you only share the unmodified value so a 10, perplexed to 11 would only share the 10 to other figures.

Hope that helps.