Suspension experts.....
 

I have recently purchased a Midstates Cobra and in the little bit of driving I've done it seems to easily bottom out. Believe car has the standard Midstates/Shell Valley setup(Qa shocks, coil overs and nine inch rear) using 350 front and 250 rear springs. Since I intend to get the car corner balanced and aligned can anyone make a suggestion ie 300 lb springs in the rear, or longer 250 springs? By the way the car is a 351 small block.

I was hoping that some suspension experts would have replied to your question ... I'm interested too.

The first step is to get the car corner weights, travel calculations, etc.
Many sites have information on how to set up a suspension, see QA1 link.

http://www.qa1.net/qa1_motorsports/images/drag_tech.pdf

My Cutting Edge Replicas was set up way too stiff. Bounced over small bumps and felt like a skateboard. Brought to a suspension shop and had it frequency tested. The frequency was very stiff at over 2 (close to Formula 1 car frequency!). Long story short, new Koni's, new springs (rear 600 to 450, front 500 to 350) 2-1/2" to 2-1/4", very drivable now. $$$ ouch!

I've also got a Shelly Valley Daytona Coupe that was set up for the track and the suspension was way too stiff for weekend driving. Great on a smooth freeway, but too stiff for potholes.

Had 450 front (with anti sway bar), 350 rear. I am now running 325 x 10" on the front with new QA1 double adjustables, 125 x 10" on the rear with new QA1 single adjustables (just added last month). Probably should have 8" on front (recommended length for shock) and 12" on rear (long travel shock, recommended spring length - didn't have any 12" springs), possibly 150 rear. Rear 125# spring compresses ~2" at rest, no preload. Getting close and much better. Will need to test drive more.

Longer springs and no preload? Add preload to current springs? Check the recommended spring length of the shock. corner weigh the car, check wheel travel, then buy a bunch of springs! eBay! Or bring to suspension shop and pay the $$$?

I believe the QA1 site has a spring rate calculator. Check the angle of your shocks and plug it into the calculator and you should come up with a close estimate of the weight of springs you will need.
From your description and the weight rating of your springs, it seems they are way too light.