Pictures would help a great deal to give you the best answers possible.
There is a list of restorers on the home page of this website. Many people here have restored their own canoes, however, and if your canoe doesn't need much work and you'd like to tackle it yourself, there are many here who can help you through that. You may live near a WCHA member who would either restore your canoe for you or give you assistance... it's a friendly bunch!
Paint colors are up to you... Morris canoes look nice in a single-color but are also appropriate candidates for designs and several colors.
You may want to use the "search" function above to find discussions of canvas-- you'll get a thorough discussion-- more than I am capable of! If you hire someone to restore the canoe for you, he or she would have suggestions re canvas weight.
If you want a center thwart, it would have to be re-made... the only other option would be to find one that has been salvaged from a Morris of the same size. Those who restore usually re-create the missing parts.
If the eye hole on the deck is diamond-shaped, with a hole in the middle, that's a flag or pennant holder. Some people put a rope through there and attach it to a painter ring on the stem... but originally it was meant to hold a little flag, if I'm understanding what you are describing.
Kathy