C:\test>perl -ple"$_ = join '|', m[(\s*\x22[^\x22]+\x22\s*|[^,]+)]g"
988A5521, 98_1V_HB, Hel Product Pool (Pds Dd), false, store, false
988A5521| 98_1V_HB| Hel Product Pool (Pds Dd)| false| store| false
988A5707, 98_1V_HB, "Chinook, IPT ME Support", false, store, false
988A5707| 98_1V_HB| "Chinook, IPT ME Support"| false| store| false
988A5708, 98_1V_HB, "Chinook, ME Factory Supt", false, store, false
988A5708| 98_1V_HB| "Chinook, ME Factory Supt"| false| store| false
988A5761, 98_1V_HB, Tandem Rotor Configuration, false, store, false
988A5761| 98_1V_HB| Tandem Rotor Configuration| false| store| false
^Z