Hello Clint,
From what I understand from your application, you want to go through a set of options and then finally execute a sequence depending on those options.
Like you said you can call the simple OI in case structure but it will make your application lot more complicated. Thus best thing is get the file name and provide that name to the simple OI. I can think of two different ways to do this:
1) Create a VI that gets the options and finally gets the name of the sequence file, which can then be sent to the simple OI for execution.
2) Create a flat sequence structure in LV, and in the first sequence get the name of the seq file after providing the options and in the second structure run the simple OI after providing the name of the file.
I hope it helps..
Rajiv