SOLUTION
After replacing everything in the front suspension (except the sway bar), I took my Altima to a local mechanic (Fair Auto Huntington Beach: very great guys). He let me throw it up on the lift and we started checking torque on everything I had replaced.
A couple of bolts were not to the torque spec including
• 1 sway bar endlink bolt
• 1 strut bolt
• 2-3 engine mount bolts
After checking all the bolts torque we spent a half an hour inspecting everything, and could find nothing. No sign of wear or anything loose that could be making the noise. So we dropped it and took it for a test drive and NO MORE NOISE! If I had to guess I would say that the engine mount bolts were the ones causing the noise as they were the loosest.
I could only get so much on the bolts with the car on jack-stand's in the driveway. (I'm 6'7" so space is tight) But with Fair Auto's help we got the proper torque on everything and no more front end clunk.
Although, (this may help someone else)
I was getting a Soft Clunk on the front right Strut a couple weeks later. After a lot of researching I did this:
• With the car on the ground, loosen the center strut bolt 3-4 turns

• I bounced the car up and down a little and turned the wheel slightly back and forth (the shock will move around in the strut mount and bearing a little)
• Retorque it to factory spec
• Solved that clunk issue