Option 2: Six levels of spell to prepare (maximum spell level 3)
stacking rules only applies to 'bonuses' which have an overloaded meaning that limits it so it does not apply to all positive effects.
Bonuses are numerical values that are added to checks and statistical
scores. Most bonuses have a type, and as a general rule, bonuses of
the same type are not cumulative (do not “stack”)—only the greater
bonus granted applies.
As for picking between option 2 or 3, I do not have a rules citation. However, since the spells are cast separately, I could only imagine that the effects are separate and you would get to prepare up up to 3 levels of spells twice. Further, I would not allow a player to turn 2 level 4 spells into 1 level 6 spell or 3 level 4 spells into a level 9 spell. That just seems way to powerful.