Got the same exact problem on my truck,its a 99 5.9L,got it last august.
Heater core had a leak a month after I got it,replaced everything,heater core,blower fan,a/c evap,thermostat,water pump and even the fan clutch.
Have had crap heat all winter,and it sucks in the mornings big time.
Is there anything you can run through the cooling system to clean out the block?

 

From what I can tell from diagrams and experience...

Water is pressurized by the pump into 2 channels,
goes through each cylinder bank,
through each head,
and joins at the passage in the intake.

From there...
some to bypass then to pump
some to heater then to pump (this fitting has 'pressure' when disconnected, this stumps and intrigues me)
and sometimes,
some to radiator then to pump.

Doing a timing chain tomorrow, will be able to experiment while draining and filling.

 

Yes there are treatments made by many of the same manufacturers that sell the various types of coolant.

I did a flush using these products TWICE on my Ram 360 and neither made a bit of difference.

My next system fix is filling everything up with vinegar. The block and radiator. The vinegar should help dissolve any buildup in the block. I may follow that with a fill up of CLR, then thorough flushing.

 

For what it's worth...

I was 'inside' my engine this weekend, timing cover off, water passages were clean as a whistle. I really don't think the blocks/heads are the problem here.
Recovering from chain replacement, I filled the return heater hose until the return fitting spewed and shoved on, same with radiator supply hose, drove, no heat! There had to be water in there!
While pump was off, I chased and blew though both bypass and heater returns. Seemed the same flow, my replacement impeller has a disc with large 'hole' against pump body/return feed zone. Hole feeds impeller 'fan blades'. Hard to imagine this not working.
Anyone working/knowledgeable on thermostat bleed hole / water or steam vapor locks on this system?

 

I always put holes on my thermostats. I have (3) 1/8" holes in the one I currently have on both my Durango and Ram.

As a side note, my Durango core doesn't gurgle. My Ram core does. Neither have heat, and both have air holes in the T-stat.

 

I replaced my clutch fan setup with an electric one,noticed a difference of better heat in my truck from this.Not sure if it was coincidence or not.

 

Still fighting it.

Tried a new radiator cap, convinced myself an old seal could cause no burp/cool/fill. 4 or 5 cycles later, no change. Took stat out, drilled 2 small holes, filled all hoses to overflowing before assembly.

As it warmed the first time... I saw some bubbles, I had seen them before and discounted. I would say pancake cooking rate and size in the 2 sq inches of radiator hole. Looked for videos of others troubles with head gaskets, this is nothing. But - I wonder if it's enough to airlock the heater. A large 'rev' will suck coolant down, and then rad appears over filled as it calms down from rev. Ended with hand clamping top hose (almost burned, stayyed red) for the seconds to put cap back on. The top hose just never seems to fill full to me - ya' know hard with fluid pressure rather than gas pressure. I have to believe if it's not full then the heater never really is either.

I'm debating a pipe tee, arranged so top of tee leg is highest thing in system. Anyone tried that?

 

Is this issue mostly or only with the 5.2/5.9 blocks? I had a low heat prob with my 4.7 when we first got it but it was a simple repair. The nitwits the original owner had work on it routed new heater hoses up over all the emission hoses etc being lazy, that caused them to be higher than the fill so they didn't have a/f flowing through them. I would guess air locked and unable to burp. re-routing to the correct position solved it but my system is different than the 5.2/5.9..it is really particular about being filled and burped though...even at that it's exactly as tshepard describes, never seems like it's completely full, adding more a/f just overflows the reservoir. Regardless I have great heat, front and rear. Could this be scale buildup in the rear head ports like older chevy small blocks can have? Those wouldn't unclog often with flushing either....IINM that causes the coolant to flow into the bypass rather than through the core...

 

This seems to be a 5.9l issue only. The 5.2 was nearly identical, just different inside the passages from the 5.9l. The 360 was developed like 5-7yrs after the 318/340 block as a smog motor.

 

Ty for clarifying