The one valve was higher because its stem was bent and it will not fully seat into the valve seat.
You are being hosed - they screwed up the timing when the installed the new chain and did not check the basic timing before they attempted to start the engine. This is a HUGE oversight on their part.
They should fix this problem with NO cost to you. The only question in my mind is wether or not they are competent to fix the damage they have done to your car. Based upon their results of a timing chain replacement I would say NO.
Has this shop done work for you before?