I have not used Aquafold before so I can't tell you exactly. However I have tackled a similar problem once before.
I once created a Powershell script. It opened a ODBC connection to my database and then executed stored procedures in a loop until end of file.
I suggest having a text document with each line being the name of an Stored Proc to run. Then in your powershell script read in a line from the file concatenate it into the call to execute a stored procedure. After each execution is completed you can delete the line from the text file and then read the next line until the EOF (end of file) is reached.
Hope this helps. If I have some time this morning I will try and do a working example for you and post it.