Upon transfer, you essentially had a gift/sale transaction. You sold your son 1/3000 of the property for $100. At the time your basis in that portion was $50. So you should have reported a gain on that portion of $50. You also gifted him the balance 2999/3000.
Your son's basis in the property is your basis in 2999/3000 of the property or $149,950 plus his purchase price on 1/3000 of $100. Thus his basis is $150,050.
It takes us a while to get the whole concept. We did not know that in giving this land as 100% gift, no amount of $$ has to be put on QCD. We have just found out. So the $100 defeated our purpose. Is there a simple way to correct the QCD to eliminate the $100.
You are sharp.
It would be difficult to reverse a recorded transaction that happened in a prior year. This $100 amount is nominal and was used for recording the transfer, not for income or gift tax purposes.
When you filed your gift tax returns you probably reported 100% of the property as being gifted. You should be aware that if your return is audited you may need to explain the transfer. However you would only owe $7.50 in federal tax (15% of $50). plus interest and penalties.
As your intent was to gift your son the property, he should use the $150,000 as his basis.