lol, just keep testing water and do water change if you see ammonia spike

the filter will keep up eventually but it might take a bit of time. Plants help too.
That's the pre-filter I'm talking about, mine is just DIY
I guess your tads are bullfrog tads, are they huge and greenish and spotted?
1. I think it depends on you. I think some people want to control their plant so they kept them in pot to easier maintain/cut back/fertilize if need be. I think for lilly, if you let them loose they might take over the pond easily lol. I have mine contain so i can move them and cut them if I want since my pond is small. If you want to plant them in the pond without pot, pea gravel or just stick them in between the rocks will be the most benefit for your pond (the roots take nutrient from water directly)
2. I have read about this on here a while back, that the clams can die and will pollute the water and the hardest part is to find which one died. may be you should search the forum for this
Anya