I have a ZZ502 with the GMPP intake manifold and an Edelbrock water pump (long). Does anyone know if it matters as to the size of the thermo bypass hose (from the pump to the intake manifold), does it have to be either 5/8" or 3/4" hose? Also, the manifold has a center-front position for the connection, but there is also two more cooling system ports located in the manifold at the #1 and #2 cylinders. Can these be connected to the thermo bypass hose instead of the center position? Also, The clearance is tough with my setup. Thanks for the help,

I think the oem bypass was 3/4" but either size should work OK. The port at #1 is for a temperature sender. The port at #2 is for a heater hose.

5/8 should be fine for a bypass----just get some 5/8 nippples and go for it.
If the intake and the WP are threaded deep enough, the shorter 5/8 nipples give a bit more room to bend the hose w/o kinking it.

I use the hole at #1 for a temp sender
I use the hole at #2 for a cooling fan switch

And I use the second hole in the front of the intake for the heater hose feed.