In my sector salary negotiations come after interviews.
No of course it's not too late! Sounds like the headline salary is ok but the whole package adds up to less?
Do they know your current salary?
From their pov they have gone through a long process and picked someone they want and to go back and think again is apita for them.
Stick to the email contact you have- email back and say thanks for the contract you've reviewed it and would like to discuss. Ask who to do that with and contact details/ is it hr (they might prefer to have hr in the middle).
Be straightforward. The salary is fine (if it is) but the overall package does not meet your expectations. Tell them it's 10% less than your current package. See what that makes them do.
They may not have wriggle room on the benefits package and if so then fine, happy to make up the difference via salary.
Ask for details of the share scheme.
Bottom line is, depending on industry of course, 5- 10% on salary is not a big deal.
Once you are in, no matter what they promise, you are very very unlikely to see any decent increases.
Good luck!