Your LS400 will see this on the following upgrades...
Intake nothing, try a BFI intake...Cheap and the best...maybe 5hp
Chip - you mean ECU piggy back - 10-15hp...
Magnaflow mufflers resonators - 10-15hp...
I personally would do the mufflers and cat converter using both with magnaflows...The y design in the Magnaflow cats really flow well and the resonators do nothing but help reduce exhaust noise...Those are used for noise control... The cat and muffler upgrade will bring you maybe over 20hp and you will notice a good difference...
The best upgrade you can do is the upgrading you torque converter from stock...Good luck..