skip the baking soda and take a few Tums instead.
the calcium carbonate you said you have will work just fine as well, considering that it is the active ingredient in Tums.
Tums are generally approved by doctors for long-term use; however if one was popping multiple antacids per day, one should seek the source of the heartburn...but, that is not the issue at hand here - to summarize, yes, it is okay to have a couple of Tums per day long term. It is not recommended to exceed 7500mg of calcium carbonate in 24 hours.
The only possible long term side effects I could find were possibilities of either constipation or diarrhea, which would resolve itself upon cessation of taking the supplement.
Since you are obviously seeking to have the amphetamine stay in your system longer (hence your inquiry about taking baking soda/calcium bicarbonate) it's important to take the supplement WITH FOOD. When taken on an empty stomach, the supplement will only alkalize the stomach acids for a short amount of time (approximately 30 minutes.) Where as if you take the alkaline supplement with food, it will keep the stomach acids at bay much longer (approx. 3 hours.)