Is my donor area over-harvested? Can this be fixed by placing grafts into the bald patches? (photos)

The only way to tell is to wait about 2-3 months.  But in general, your donor zone looks very depleted and looks like there is a possibility it may be permanent.  Unfortunately this is the risk taken with FUE, especially when it is done by an unqualified clinic/doctor.  Fixing this by transplanting grafts into the depleted areas is possible but extremely difficult and labor intensive.  In the last year I have started to correct a lot of procedures such as yours by transplanting grafts into the depleted donor zone with hair taken from the beard or chest as well as micro pigmentation.  I would recommend finding a skilled surgeon in your area that could help you.

It will be very difficult to answer this question at this point. 
I would start immediate treatments with Laser Cap to try and get all the hair back into the growth phase as quickly as possible.
Sometimes when an area is over harvested it can create shock loss all over.
Have you let your Doc know the concerns you are having? If not, I would start there and see if they can assist with treatment.

It may or may not be patchy when it heals. Only time will tell. You cannot tell with photos alone.3500 graft FUE is considered a very high number of grafts harvested at one time.  It may lead to patchy looking donor area when you keep your hair buzz cut.  It may even out with time and longer hair.

First
of all I think that you have to wait because 10 days is a very short period.
There is a possibility that you will have more hair to the donor area in the
future. In case you don’t see any improvement, theoretically you could do hair
transplantation to the donor area but the problem is where the grafts will be
taken from. Probably, there are some areas which could help as donor areas but I
don’t think they will be enough for resolving completely your problem. Probably
you might start considering of micro pigmentation. Anyway don’t be pessimistic
and wait for 4-5 months until you see the final result and then you can decide.

Below are two critical questions that you need answers to before moving forward with an FUE clinic.  1) Is your Doctor the person doing the FUE harvesting or is a Physician Assistant or technician doing the harvesting? 2) How long has your surgeon been doing FUE and FUE harvesting?