What are the puffers? If we're talking figure-8s, then the salinity need not be very high, at least to begin with. Even SG 1.003 will be fine. At that level, it'll be freshwater filter bacteria, so go ahead and use some filter bacteria from another tank.
I'm not convinced about there being "brackish" bacteria at all. The brackish water habitats in the wild are variable salinity ones, and my guess is that there are varying populations of fresh- and salt-water strains that bloom or die back as the salinity changes. I believe this is what causes the nitrite spikes. In the wild, where the fish load is low, this wouldn't be an issue. You don't get nitrite poisoning in an estuary since the water is constantly being washed out to sea anyway.
Once you have the tank cycled at SG 1.003 for a month or so, you can then slowly increase the SG and monitor the nitrites.
Cheers,
Neale