You do choose which replacement effect to apply first, but which one you choose won't make any difference here. Either way, you'll get two counters from
Master Biomancer (assuming nothing else is boosting it) and one for each time you kicked
Joraga Warcaller. No more than that.
Replacement effects work by looking at the very next set of instructions the game is about to follow and modifying those instructions before they can be carried out. The instructions are modified again and again until no more replacement effects want to apply, and only
after that whole process do you actually follow whatever the instructions ended up being after all the modifications. Applying the replacement effects from
Joraga Warcaller and
Master Biomancer don't put the counters on the Warcaller immediately–they modify the game's instructions for how to put the Warcaller onto the battlefield, which won't actually happen until both the Warcaller and Biomancer are done editing.
Since
Joraga Warcaller's elf-boosting ability only functions while the Warcaller is already on the battlefield, and the Warcaller doesn't get the counters or enter the battlefield until after all relevant replacement effects have been applied, there is no way for a
Joraga Warcaller to boost
Master Biomancer's power in time to put additional counters on itself.