So I have this fl250 with a modded cage and a different seat. But the seat always gets way to hot.

I will get better pictures tommorow

Here is a better pic of the entire machine.

Do you have a heat shield between the seat and Engine/pipe?

I have a heat shield from auto zone and aspestis on the exhaust.

Nice machine I like the color.

Looking at your machine (as well as any other oddy) I see a design flaw.
The Engine is behind a seat and that seat causes a vacuum, just like the hole in the air your car or a semi truck causes when you are driving down the highway. This causes the air to move foreword toward the seat. That's why your car rear window and back end is always full of poo.
You can try to install air deflectors just like the FL350 has. Honda did this to get air to the Engine to try to cool it down by providing air flow to an air cooled Engine. It was a pathetic attempt to fix a design boo boo (putting an air cooled Engine directly behind a wall).
All race cars have ducting to cool brakes with air flow.
Try it -- you got nothing to lose.

Go to the car wreckers and try and get some of those perforated heat shields they use underneath around the mufflers etc Get enough to cover your back seat.Way better than just solid metal sheet which is a heatsink.
Also get some header pipe heat wrap tape to minimise the heat transfer from the header pipe.
Also yes on the side air scoops plus a fan too if need be?