@TheRealYeti ,
I'll attack your question from another direction, your script might be inefficient. I have seen scripts that took hours to run, rewritten to run in a minute or two. Without more details, it is difficult to assess that.
Given that you know vb6, you could get the user input and your script could generate a JSL script to do the work, but run it via VB6 that uses DoEvents. I do not know that function nor am I a VB expert.
The JMP documentation "Automation Reference" points you to many of the JMP library functions exposed to VB.
To create a JMP session and make it visible, add the following code to your VB
script.
Dim MyJMP As JMP.Application
Dim JMPDoc As JMP.Document
Set MyJMP = CreateObject("JMP.Application")
MyJMP.Visible = True
The JMP library function, Run JSL,
Run JSL file
Not sure if any of that helps.