I have a 91 Indy 500 SKS that appears to sit low (11 inches from the ground to the tunnel in the rear) when I take it off the stand. I had a spare shock (new) so I replaced it, no change. I followed the suspension adjustments in the Clymer manual (measured the sled height unloaded then sat on it as if riding and adjusted so the difference is within 3/4 of an inch). Still seems low and when I go over a steep mogul it sounds like the track scrapes the tunnel in the rear. Any suggestions?

I would try replacing your rear springs,the two in the rear on the sides and the one around the front shockin the rear,other than that you won't get a whole lot more out of it unless you install a newer suspension.
the spring change will probably help out your bottoming problem though,a lot of people never change these parts and wonder why it does'nt ride right,i change mine every 2 years.

What would be a good suspension to upgrade to?

What hole are you bolted on??

Where the rear suspension bolts at the rear there is 2 mounting options,one in the tunnel another on the bracket below the tunnel

I mounted my 91 Indy 500 on the lower holes that made the rear higher and better in deep snow

travel is 7.75"inches on the 91 Dial Adjust rear suspension

I'll check tonight after work. Where is the travel measured from? If I measure from the ground to the bottom of the tunnel I get 11 3/4", when I sit on it measuring in the same place I get 11'", after adjusting the tension knob.

How does it ride though? Its never going to be as high as new sleds, it only has about half the travel.

The ride is a little spongy and it bottoms out on the bigger bumps. I can pick up the rear of the sled 4-5 inches with no effort and when I let it go it drops back and stays there. I have it bolted to the second hole on the bracket below the tunnel and on the lower hole on the tunnel itself.
Needless to say I've adopted a standing riding style that works well as long as I don't have to stop in a hurry say for a moose or I go flying over the bars, not like that's ever happened though :D .

If you already replaced a shock i'm still willing to bet that your springs have no spring left in them.

Sounds like a plan. I ordered the springs this afternoon, hopefully they will be here Friday so I can mount them and see if it improves. I'll let you know how it goes. Thanks