It may be there is a leak in CO2 system at some point that's causing your problem with changing bubble rates. It's pretty common with DIY set ups to have leaks, either at the bottle cap/tube interface, or any other tube connection along the way.
There are some really neat miniature bulkhead fittings you can get that work extremely well for making air tight connections from a bottle to tubing. Meant for gas line to gas tank fittings in some model engines, the ones I've seen are plastic, made by Four Most. Not very costly, two sizes. The tubing used for the gas lines in the models is the same as the silicone version of air line tubing and either size works, though the larger one may be the better for this purpose. The smaller one is 1/8", I forget what the larger one is, only very slightly larger in any case. Packs of two.
I don't know how long a citric acid/baking soda bottle would last, but have been wanting to try it, if only because it is less messy, with no by product ( alcohol from yeast). But I think a comparably sized soda bottle would last a bit longer than a yeast bottle would, if only because the alcohol kills the yeast before it has a chance to 'use' up all the sugar, so the soda/acid mix is more efficient.