[Hydro]

You didn't mention the year of the truck or model

Bubbles can come from a damaged suction line or a restriction in that line
when you changed the filter in the HFCM, did you lube the o-ring? and turn the cap until it bottomed on the threads?

The fuel bowl should fill within 3 to 4 seconds

it is also possible you have a clogged inlet line at the fuel tank, some of the metal tanks liner would flake off

It is normal for the pump to time out in about 20 seconds without the engine running -- when the engine runs, the pump is continuous

 

[Hydro]

Dropping the tank is pretty easy as long as it is near empty
you can loosen the passenger side bed bolts and remove the driver side
then tip and block the bed up a little, to get to the fuel pickup

Ford picked a really dumb spot to put that lower filter for sure
you need to grease the o-ring and be sure it is not "twisted" on the cap
the cap will bottom on the threads, unless someone has forced it in the past -- there is a stop on the threads

I have seen the pickup foot in the tank disintegrate and lodge pieces inside the line
so if that is the case, you would need to blow out the line with air pressure

 

[Hydro]

Check the suction like from the tank to the hfcm for damage / pinched places
had a critter that bit my suction line and was not very obvious the damaged spot, only tiny puncture marks

You can substitute a 3/8 clear line in a jug for a suction setup to test if the bubbles go away

Some fuel bowls drain back(they are not supposed to) and when you do a filter out test, there may be bubbles
if you continued to run the pump the bubbles should clear up, would need a catch pan for the excess fuel tho

 

[Hydro]

You want to keep the filter in the hfcm, the line is just to eliminate the current suction line in case there is damage

you can add a second line on the return from the hfcm to the jug to eliminate the tank lines all together
the clear lines will let you see if the fuel runs clear or not - do this with the filters all in place
the 3/8 clear hose fits the connectors pretty well, but you still need a clamp

 

[Hydro]

Did you tighten the filter cap till it bumped end of the threads? -- internal stop
air could be if you didnt fully seat the filter o-ring
or possible the o-ring where the pump motor goes in the housing

Not following on how you have the fuel lines arranged, can you give a better description?

Fuel flow out of the pump should fill a soda bottle in about 10 seconds, maybe less

Further thought: the pump can draw air thru the return line, if the tank level is low or the upper fuel filter is not filled
basically inside the HFCM the return is connected to the pump suction, there is a valve that should be closed at these temps, but may be leaking
you would need to cap both return fittings on the HFCM
@TooManyToys has a good video of the insides of the HFCM and how it works

 

[Hydro]

Ahh, then cap both return ports on the HFCM, likely pulling air from the return, either thru the tank or the filter housing

The low flow is concerning, just had mine off a while back to check how low it would go before I was out of fuel (138 miles ...lol)
anyways the fuel flowed out of the line about 2-3 inches with the line horizontal
this all depends on if you have a restriction in the tank or in your line adapter
you could place the end of the clear line an a clean container to see if the pump flow increases

The pickup foot is gone in my tank, that is why it runs out of fuel at 138 mile -- the after market foot is not of quality so I am told
so looking into a sump kit, or possibly making a sump -- I have the tools
just can't see boring a 3 inch hole in my tank, ...lol

 

[Hydro]

I checked the amount of fuel it pumps when cycling the key on. I cycled it twice it pumped out just under 8 ounces of fuel.
I also rechecked to make sure I had the right torque on the cap.
I'm not sure if I need to mess with the air bubbles too much more at this point. If it looks like I need a new pump, I'll end up going through the hfcm anyway.
Ideas?

There is not a torque on the filter cap -- it is until it stops turning, there is a stop on the threads unless it has been broken
it is a definite stop

 

[Hydro]

The pump can suck air down the return line from the upper filter
under "working" circumstances that line is filled with fuel,
since the pump delivers more fuel than the engine can use

Did you look at @TooManyToys HFCM video? shows how the inner workings of the pump