Thanks so much for the responses. No, there is no business class on the Manado-Sorong leg and Lion Air is the only game in town on that route. I am hesitant to wait to get to the airport and try to sort it it there. I think we may have solved the problem by flying Citilink from Manado to Mankassar, overnighting at an airport hotel in Mankassar and then flying Batik from Mankassar to Sorong.
I would suggest Garuda instead for this. Manado to Makassar to Sorong. Garuda also gives you 23kg excess per person for "sports gear". And if you have silver, gold, platinum status on one of their partner airlines you will probably get extra kgs as well. Although the Garuda flight departs to Sorong at 2am, you can stay in the airport hotel before that