I'm having trouble picturing 3.5" spiral flows to a 3" side pipe.
The "muffler" insert goes in the 3" side pipe. If the flow tech shorties are not 1.5" primarys you can use them as the start/primary. Some of those shortys have small pri tubes size. should be 1.625" outside dia minimum.
The hedmans are a good buy and can be customized too.
this is the basic 4-2-1 long tube Y collector configuration