there is currently no option known to cast a /castsequence with diffrent targets
Because the options (like the target, modifiers) are defiend for the hole castsequence not the individual Actions of the sequence.
(as far as i know)

Only thing you could do, is to have a static "unit" for the castsequence like the focus, and change this unit, between the keypresses of your sequence.

Example:

Castsequence makro (bind to "2"):
/castsequence [target=focus] Lightning Bolt, Healing Wave, Water Shield

Another makro (bind to "3"):
/focus [nomod,target=party1target];[mod:shift,target=party1];[mod:ctrltarget=player]

Then you could press the following for the "sequence":

3,2,"shift+3",2,"ctrl+3",2

but honestly, 3 simple buttons (or one makro with 2 modifiers might be simpler, like:

/cast [target=party1target,nomod] Lightning Bolt;[target=party1,mod:shift] Healing Wave, [target=player,mod:ctrl] Water Shield

)