Is the radiator getting hot when the stat is open.
Check it all over, and especially the top corner by the fan switch.
If the rad is hot then the pump should be working. If its cold in just the area of the fan switch then you have trapped air.
My fan cuts in and out at just above 90 and keeps the temp bang on 90.
Have you made sure the fan works by bridging the wires / terminals on the fan temp switch.
I'm not sure the small pipe being blocked will cause your problem but could be wrong. The secondhand one in my shed is also blocked and it seems to be blocked with something more solid than dried up coolant. Cant ever remember seeing water coming out of the one on my car either. not when running or when sqeezing it to bleed the system.
Could be still not be bled properly, a faulty pump, faulty fan switch or wiring, or a faulty new thermostat. Where did you buy the stat from. Heard many stories of faulty stats from ECP and GSF.
Paul