The hose routing (photos B and C) and tight loops suggest they could be causing some fuel flow restrictions, which would support your theory of the pump overworking/overheating. Maybe you could make some adjustments there, and possibly use hard fuel lines to prevent this.
Last year, I installed a Holley sniper EFI on my 3.5 and opted for an in-tank pump to replace my OEM low pressure pump. I used Bosch fuel pump 68006 and its fuel strainer 69225 for about $60 online. It mounts in place of your OEM pump on your sending unit inside the tank, keeping the pump cool and providing plenty of pressure at 60+psi. I am not sure if that is an option for you, given your tank style. (mine is on a 110 rear tank).
That said, the holley EFI system did not turn out to be near as reliable and "turn key" as advertised, and I've had some occasional glitches/malfunctions. I'm moving on to diesel..

 

Thanks for the input.

1) With an in-tank pump like the Bosch 68006, were you concerned that if the fuel level drops below 1/4:

• it can cause the draw tube to suck air?
• without gasoline to surround and cool the pump, will the pump overheat and get damaged?

2) This pump, the in-tank pump for the RRC 1986-1990 and Defender 110 NAS 1993 fits in my D90 side tank, but it's only 35-37 psi of fuel pressure. My Holley MSD Atomic EFI 2.0 needs 60 psi I wonder if there is something similar that can fit in my tank or if this can be modified

 

1) I had no issues at all, this is the same fuel pump as installed in many cars and trucks etc. It does not suck air unless you run it empty or if it is not installed properly in the sending unit. I had no overheating issues, it's the same set up as every other vehicle out there.. The pump is at the bottom of the tank just like the factory set up.

2) I took my old sending unit assembly out of the tank and simply swapped the pumps, which required connecting a hose and a couple of wires. easy swap.

 

You need to verify that your fuel tank is vented properly.
A poorly vented fuel tank will cause all the symptoms you describe.

 

Thanks for the input. I have a pretty new, vented, fuel cap. I may consider taking it apart to check that it's working properly.

 

Update and Hopefully Problem Now Solved

(I’m not an engineer or mechanic so all these points above and below in the posts could be great advice, terrible advice or in-between so make sure to consult experts).

1) GAS CAP VENTING. I first drilled some holes in the underside of the gas cap after taking it apart as detailed here. (See Photo D for where I drilled holes in metal assembly only, not round metal closure, round metal/rubber flange or plastic cap. I did 4 holes, although maybe 2 would be enough, maybe start with where 2 red arrows are, and make sure to remove flange and collect all shavings). I just used a drill bit on-hand and applied a bit of pressure as it was soft metal and pretty easy. Some take another approach like drilling a small hole in the metal filler tube close to top of cap. Poor or limited venting as suggested could’ve very well been part of the problem. After doing this, when I now remove the gas cap, I no longer get the release of either air pressure or sometimes a mist of fuel. Unfortunately though, the engine would still stall after 30-45 minutes of driving, but seemed a bit quicker to recover with this gas cap modification.

2) FUEL CAVITATION. It seems like a main reason of my stalling had to do with fuel cavitation or what some also refer to as vapor lock. This is a good summary of what cavitation is and what seems to be the problem I was having. In short, my external fuel pump was in the wrong place (too far from tank and with a hose run with too much bend) so the pump was working too hard and eventually over-heating and/or causing the fuel in the line to over-heat and boil.

2) SOME TAKE-AWAYS. I consulted with multiple sources including the tech help line at Holley regarding their MSD Atomic 2.0 EFI system. This summary on efi installs was an interesting read. Some things that were shared along the way if going with an external fuel pump, (1) keep the hose run from tank to fuel pump as short as possible (ideally less than 12 inches) and with limited turns (ideally none), (2) keep the fuel pump at or below the bottom of the fuel tank as the fuel is meant to be gravity fed from the tank to the fuel pump, as these external pumps are apparently pushers not pullers (while that is fine advice, the fuel feeder exit tube on the D90 side mount tank in particular is on top of the tank, not the bottom, so even if the fuel pump is mounted at or below the same level as the bottom of the tank, it is inevitably doing some pulling down from top of tank and contributing to make the external fuel pump work harder). If you ultimately do need to plumb a 90 degree hose turn before the pump, while not ideal, that alone wouldn’t necessarily cause cavitation, just maybe shorten pump life by some amount of time because it’s working a bit harder.

3) THE SOLUTION. I ultimately went with an in-tank pump. When there is an easy enough choice, most prefer this location as the pump stays quieter and cooler, and less hose turns are needed with the hose line when it leaves the tank. Probably some of the reasons most oem fuel pumps are in-tank and last longer too. That said, when there is not a great or cost-efficient in-tank retrofit option, a number of folks go with the external pump and it’s obviously easier to service too if there is a problem.

I bought this feeder tube assembly which fits with my side tank and then had a local mechanic lengthen the feeder tube and swap out the low pressure carb pump with the Bosch 69225 high pressure efi pump and 68006 pre-filter fuel pick-up sock. I’ve taken the D90 out for a 1-hr highway drive and had steady 60 psi fuel pressure. No stall. Seems like problem is hopefully solved. Some other random work. I put in a new post-pump 10 micron filter (I used this Holley 731166ERL) as the old one may have been clogged. I swapped out a few worm clips with t-bolt clips on the return line and a couple of return line hose fittings had white pipe fitters tape which I was told isn’t great because tape bits could loosen and clog the injectors and instead should use a liquid pipe sealant, maybe something like Earl’s D024ERL.

Thanks to all for the assistance.

 

Further Update. The custom in-tank efi pump solution ultimately didn’t work for very long. In less than 500 miles, the pump failed. I replaced pump and it happened a second time. A local mechanic who did the work could not figure out why. I then pivoted to an external efi pump again, this time mounted below the tank and instead of using the feeder tube on top of the tank to draw fuel from, we used the drain plug on the bottom of the tank to draw fuel from. This fuel draw location allows the external pump to be gravity fed.