I am able to do commands such as ls and pwd so I can perform some unix commands, but I don't have GnyWin32 in the path. Do I need to download Coreutils?

You're using bash in cygwin but saying a windows batch file would be preferable but exploring adding coreutils... what language can this be in? I'm afraid you're out of luck when it comes to a .BAT file unless you can hunt down those guys who made as400 batch files... they did things I didn't know DOS was capable of.

Is a bash script an acceptable solution?

If you have perl, this would be a simple program to come up with.....you can just grab all .txt files, then open each of them, and read it in print out as needed, and once you see for example 2 blank lines, stop getting data.....

Sorry I didn't get back sooner, The shell is BASH. It was suggested to use ADO instead, any thoughts?

What I forgot to mention is that I need to read in the numbers at the end of each line. They represent percentages so the values can vary.
EX: 100.00,0.00,0.00,good

I came up with a vb script that reads in the data but doesn't stop at the blank line of the input. Also every thing is put into the first cell of each row.
The typical line will have the following: What is in the () would be the in the 2nd cell of each row of the csv file, I want to eleminate the dashes anf the words "Functional Aggregate". The other issue is that some rows may have the "Functional Aggregate" and the AAAAA026 switched around.
AAAUSA-0057 (AAAA CCCC) - AAAAA026 - Functional Aggregate,100.00,0.00,0.00,good

The output needs to look like the following:
AAAUSA-0057" "AAAA CCCC" "AAAAA026" "100.00" "0.00" "0.00"
this would be cells A1 - A6 and so on.

This is the VBS code I have so far.

Const xlGeneralFormat = 1
Const xlNormal = -4143
Const xlLastCell = 5

Dim sFiNa
Dim oFS
Dim oExcel
Dim oWBook
Dim sTmp

' Text file to work with

sFiNa = "FunBusAgg"

Set oFS = CreateObject( "Scripting.FileSystemObject" )
sFiNa = oFS.GetAbsolutePathName( sFiNa )
Set oExcel = CreateObject( "Excel.Application")

oExcel.Visible = True
' oExcel.Whatever = False

sTmp = "Working with MS Excel Vers. " & oExcel.Version _
& " (" & oExcel.Workbooks.Count & " Workbooks)"

oExcel.Workbooks.Open sFiNa, xlGeneralFormat
Set oWBook = oExcel.Workbooks( 1 )

' oExcel.Range(oExcel.cells(1,1),oExcel.cells(100,1)).Select
oExcel.Range( oExcel.cells( 1, 1 ) _
, oExcel.cells( oWBook.Sheets( 1 ).UsedRange.SpecialCells( xlLastCell ).Row , 1 ) _
).Select
oExcel.Selection.TextToColumns oExcel.Range("A1"), xlGeneralFormat

' save as XLS
oWBook.SaveAs sFiNa + ".csv", xlNormal


' oWBook.Close
' oExcel.Quit