IMHO - that video doesn't indicate a bad head or head gasket. Again, IMO the bubbles would be much more severe and consistent or a big bubble that is cyclical following rpm's.
Did you ever get a vacuum reading at idle and say 1500 rpm's? Take a look at the attachment. It is some great info on diagnosing engine issues based on vacuum readings - thanks to wiki editors!
That surge sounds like a vacuum leak, bad IAC or bad EGR valve.
Now, guardedly, I'm going to give you some advice that is basic, at least to me. You put a new engine in this truck and reused the old (2 yr old) water pump? It is like reusing the old spark plugs as far as I'm concerned. Basically, new engine means new plugs, rotor, cap, water pump, t-stat, etc. AGAIN, IMHO!
I noticed alot of RTV around the t-stat housing. I'm not a big fan of smearing RTV around the t-stat housing. I prefer HiTack or similar because the gasket should do the sealing and excessive RTV can cause nothing but issues. It is the RTV that you can't see on the inside of the housing that can cause issues. Probably someone will chime in and disagree with me on that though.
New water pump - less than $50, get the t-stat out and see if the problem goes away by driving it back and forth to work. If it is 15-25 degrees outside, then it shouldn't blow good heat with the t-stat removed under normal driving/cruising speeds - dress warm. And CHECK THE VACUUM!
p.s. A vacuum gauge is a cheap tool that can be used on every gas engine to diagnose problems. It doesn't matter if you're working on a 64 Nailhead, 89 SBC or a 2010 LS engine - the vacuum gauge doesn't lie.
Good luck and keep us posted.