Hi S...if I'm understanding your post correctly, you looking to put the puffers in the 29-30 and the other fish (goldfish, pleco) will move to the 55? The reason I ask is that dwarf puffers generally do better in a puffers-only tank, although there are occasional cases where dwarf puffers do well with other fish. It seems though, that otocinclus (otos) get along with puffers pretty well in planted tanks. I believe the same is true with other puffer species also, in that they prefer puffer-only tanks.
Anyway, back to your original question.
The smallest freshwater puffer would be the dwarf puffer (Carinotetraodon travancoricus)...which grow to about 1-inch. They can usually be stocked 1 for every 3-5 gallons, but this depends on gender ratios and individual personalities. Having multiple DP's usually requires having plants/decor that will break-up lines of sight, so they don't fight over territory issues.
A wonderful site to research these cuties is: http://www.dwarfpuffers.com/
If you're looking for freshwater puffers larger than one inch:
25g Marineland Eclipse (30w T-8 ):
- java ferns, anacharis, corkscrew vals, giant hygros, marimo balls, java moss
- zebra danios (5), otos (2), others TBD
6g Marineland Eclipse (8w T-5):
- anacharis, asian ambulia, java moss
- white cloud mountain minnows (10 = 6-7 inches total)