Bill
That 397 RWHP number is right around what we have seen with the 4 Boss 302S cars we have had on our dyno . Long tube headers will give you between 20 and 25 RWHP without any tuning changes and the a/f is still good. I have used the American Racing 1"7/8 headers and x-pipe and they have good ground clearance and only required a small dimple on one primary tube to clear the corner of the road race oil pan .
We have had a 14 Boss S on the dyno with BBK longtubes that made less power and they hang about 3/4" lower so I would stick with the American Racing setup .
The CJ intake , part # M-9424-M50CJ , dual 65mm throttle body , # M-9926-CJ65 and cold air intake , M-9603-M50CJ will give another 35+ RWHP , but you will need a custom tune
My current setup with an SCT tune makes between 465-478 RWHP on our Dynapack dyno. The power range is from multiple dyno runs on different days and some different race fuels.
I have been racing this combination for over 2 years with no issues
My Boss S does have a custom air box but we have seen similar numbers with the Ford racing cold air setup .