You should now be in a position to identify the remaining faults with your design, and to be aware of things that you may have missed out or unnecessarily included. Note these down.
Reappraise your design carefully. You have seen the problems with your original design, but that includes a number of decisions that have not been fully tested. Carefully look at things that cause confusion, at the functions that are there but may never be used, and at the odd comments made by people about the good and bad points of your design. Using your experience of others designs and the comments on your own, you have a great deal of information about what should be included, and excluded, from a new design. Come up with a new version of your system. It should incorporate all the good features of the previous prototypes, whilst avoiding all the problems that they may have suffered such as clutter or usability problems.
You should also think carefully about what you have learnt from the reading you have been doing over the past weeks, and incorporate any new knowledge you have into your new system.
You should also be aware of any changes in user perceptions of what they require from the system (i.e. the initial requirements are quite likely to have changed) and you should re-evaluate these and incorporate them wherever possible.
You should produce a few notes summarising what you have changed in moving from the prototype to the new design, and why. These will be handed in with the final system.