I decided to go with ol' faithful .. black waterfall foam (easily bonds to the smooth plastic liner and can even be used in wet conditions).
Compared to silicone, the foam is quite superior (same fish/plant safe properties as silicone). It does cost about $15-25 per can whereas silicone is like $4, but foam dries in 30 minutes - silicone in 24 hours. Foam also expands in cracks and is flexible once dry (holds tension good).
I probably coulda used a bulkhead fitting, but the drain was a last minute decision with not enough preparation.
All fixed up now though
Will go get some pictures now that everything's replanted.