You would choose the square port option and enter the size as 12.25 x 1. Then go back to the box screen and move the tuning up and down going back to the vent screen and checking the length it gives you each time. Whatever number you entered as the tuning frequency on the box screen that gave you a length of 3.625 on the vent screen is your tuning frequency for your current box.
WinISD sometimes overshoots the actual tuning freq. in slot/shelf ports like that, especially one with a very narrow dimension like 1". Tuning will often end up a bit lower than predicted.
This thread
Cab building question about shelf port length... has some math in it to correct for that as well as the link to this online calculator
Car Audio - PORT Size Calculations and Formulas for WOOFER and Subwoofer BOXES said to be more accurate.
If you're having problems with it accepting your port, make sure you have all your measurements set to the same inches or millimeters or whatever. Make sure you're telling it your port is 1 inch high, not 1 foot.
When you reverse engineer like this, you pretty much have to find a bunch of different drivers and see how they'll work in your box. Some you can toss out right away based on specs, others you'll have to load up and model against each other.
