If I flip heads for Ho-Oh EX's "Rebirth" Ability, if I only have one Fire and two Lightning energy cards in the discard pile, can I take all three of those?
No, you can only take one of each different type of energy, up to three total. So in this case you could only take one Fire and one Lightning.
Source: Dragons Exalted FAQ (2012-08-23), TPCi Rules Team (2012-08-23)

Relevant cards

Note: All applicable cards may not be listed below.
WOTCGH_12