OK. Here's the deal.
Before you cut your frame and added the hoop, the stock seat and cross member(s) were built to allow the shocks to bottom out (or very close to it) before the tire would contact anything.
Now that you've removed the stock pieces, and added the hoop, that clearance is all gone. You've closed that gap which will now allow the tire to hit the seat area WAY before full shock compression. Pretty common mistake. I know I made it in the past.
Now, to fix it.
Remove everything from the seat area of the frame. You may not have to remove the hoop, we'll find out soon...
Without the final shocks this may be slightly difficult, so I'll lay out the process and you can do what you wish with the info.
Install the shocks.
With the wheel set up in the swinger wrap a ratchet strap around the frame and attach to both legs of the swinger (towards the end of the legs, near the axle).
Tighten it down until the shocks are as close to bottomed out as you can safely get them.
Now look at the profile of the seat area and see where the top of the tire has come to rest.
At this point, I hope to the gods that you see where we're headed here
Now, when redesigning your seat are with this new knowledge keep any other parts that may be installed in the area (like a fender, please run a femder) in mind as well.
Get what we're after here now?
A couple final thoughts:
Sitting on or bouncing on the seat will NOT give you the information you need.
Fenders are good...
Safety trumps looks, but if you use your brain they work very well together.
Measure twice, cut once.
It's only metal. Fuck it up? Cut it off and fix it.
Now, get to work