LeonV

How did you check flatness/sleeve deck height?

airintake0_0

Hastings makes a straight edge you can use for checking flat surfaces along with feeler gauges.

Spartarus

Any white smoke?

Did you delete the throttle body / IAC valve coolant loop? If so, what did you do to the hoses?

Regarding your heater bypass, If you simply bypassed the heater core by connecting the ports, you should now have 2 hoses connecting the outlet on the intake manifold to the water pump inlet on the Tstat housing.

If you looped them on the same fitting, you eliminated the closed thermostat bypass loop. That would be less than good.

Can you link or post a picture of the area below the intake manifold, showing both water fittings?

This may be a very simple fix.

Also, What kind of intake manifold gasket did you use? Just curiosity there.