I speak from experience and know mistakes happen, and how easy it is to do it and still look right depends on your setup.

A guy posted here recently with the same problem and I advised him the same, as I have seen guys swap motors and make this mistake. He pmed me to let me know he did indeed cross the hoses, which is quite easy to do if you have the "U" shaped bypass hose, which to a lot of people appears to fit as it should between the two nipples on the thermo housing (see red illustration).

Looks right when hooked up, but isn't. Here are drawings showing how easily it can be messed up, with all three nipples being so close together on the engine and all three hose ends reaching these nipples in any combination and still look like they were meant to be routed that way.

The green shows correct, the red shows one possible combo of a wrong hookup that would lead to the thermo not seeing enough hot water from the head to open, at least not without a lot of running and residual heat build up eventully heat soaking everything. Trouble with that is you can actually overheat the top end of the motor and blow the rad cap with an ice cold bottom radiator hose, really making you wonder what the heck is going on.

Obviously you may have another problem. Just trying to help, and offering one possibility that does and has caused the symptoms you have described.