If my spouse wasn't on the mortgage can I use 100% of the mortgage as part of their adjusted cost basis for Form 1099-s? We split proceeds on form in half

I would assume 50% If you agreed to split the proceeds50/50, I would guess the assumption was that you were spitting the adjusted basis the same, 50/50. 

This isn't really a tax question. The total cost you both claim can't be more than whatever the total cost was, but how you split it is not for us to decide. 

There is a capital gain exclusion that might be helpful if you both lived in the home at least two of the last five years. The amount of gain you can exclude, when filing Married Filing Separately, is 250,000. Hopefully your half of the gain is less than that and neither of you will need to claim any taxable income from the sale. 

If not, you'll have to work it out. The name of the mortgage holder does not determine ownership, the Deed does. 

Topic 701 sale of home