After putting the motor back in, whenever I drive it for more than 5 minutes, I start to get the sweet syrup smell from the air duct. Heater still pumps out lots of heat. No puddling, and not really any fogging when switching to defrost. Could the heater core be blown? I understand it's a heavy replacement procedure. My temp gauge stays normal as well.

 

You're right about anti-freeze having a sweet smell. You could have possibly hit the heater core tubes that go through the fire wall and created a small leak that (for now) that evaporates before it can create a puddle and leak out.

You can do one of two things to check for a cooling system leak.
1- Do a pressure check on the cooling system.
2 - Closely watch the level in the overflow tank. Check when cold. If you have a leak, the coolant from the tank is sucked into the engine as it cools off, so only check it when the engine is completely cool.

Neither process will tell you where a leak is located. But since you can smell anti-freeze in the car, there is a 3rd option - by-pass the heater core and see if the smell goes away after a couple of days.

 

OK-Thanks DennisMik! If I decide to (temporarily) bypass the heater core, does the t'stat need to be removed from the pipe? I've read conflicting info, some say to remove the t-stat, others say not needed. Oh, I also get the sweet syrupy pancakes smell from inside the bay when I lift the hood. I'm certain that my head gaskets are ok though, and I am not getting any milky cross contamination (ask me how I know about that LOL) or dreaded white exhaust smoke so I am puzzled why the smell is also in the engine bay. Maybe it's permeating from the core-I dont know.

 

Another possibility is that the leak is not in the heater core. Smells can get sucked into the car via the air intake for the heater/ac.

As far as bypassing the heater core, that wouldn't have anything to do with the thermostat, you don't need to concern your self with that.

Something to check are the 2 small hoses for the EGR valve by #5 cylinder.

 

I bypassed EGR (00vi swap)
I guess I'll keep looking for where the leak is, wherever it is.

 

Well problem is still there. It doesn't really always smell through the heater. It does however smell whenever I lift the hood. I try revving it from under the hood and I can't notice anything leaking or steaming, so I really am stumped here. Are there any tips for detecting a leak? Like I was thinking a mechanic's mirror to check for steam/moisture from various points on the engine.
EDIT: Found some residual leakage by the temp sensor where it screws into the crossover pipe! I was able to tighten it about 1/8 of a turn, hopefully that ends it!

 

You have a tough one! I hope tightening the sensor does the trick.

If not, check all the hoses, use a mirror or something an look on the bottom side for drip marks. Examine the radiator where the plastic tank is crimped to the core, especially around the upper hose connection.