I haven't had any clogging problems, but love to problem solve. I use the unit straight-up stock, and have made 7 batches so far. Here's some pictures and measurements. Maybe with some compares we can find something that's different. I have the G4 35L US-120V system.
Mash Process
1. Heat water to strike temp with basket sitting in unit.
2. Raise basket to mid-way foot level, which keeps the bottom of my malt pipe just out of the water. I mash at 1.25 qt/lb, so on a recent batch that was 4.76 gallons for 13.25 lbs of grain (profile has 0.66 gal of mash tun deadspace).
3. Dump all my crushed grains in the basket.
4. Lower basket into the strike water, then with a long spoon, stir it all up quite well. Slowly, making sure I don't have any clumps/dough balls hiding out anywhere. I've never actually timed this step, but I'd estimate about 5 minutes.
5. Put the upper mash screen on.
6. Lay the recirc hose on top so it makes an 'L' shape with the hose end laying on top.
7. Turn on the pump 100% duty cycle, but recirc arm ball valve closed (lever at 9 o'clock position).
8. Open recirc arm ball valve enough to get all the air bubbles out of the line (about 7 o'clock position) briefly, then close it down until I get a steady enough stream. This is obviously highly subjective, but I aim for about a "pencil diameter". Not pencil lead, but the whole pencil. I guess it roughly necks down slightly in diameter from what it would be if it was full flow. I don't want it too fast to starve the bottom of the pipe, and I don't want it too slow where I can get a stuck mash (based on experience from my 2V brewing system). This has the lever at about 8 o'clock position.
9. I run lots of step mashes. Maybe 50% of the time I'm doing 100F, 122F, 145F, 168F. Other times it will be a 148F or 156F, followed by a 168F. I use rice hulls only if I'm doing something with > 8 oz of wheat or rye. And typically I use 4 oz of rice hulls if I have maybe up to 10% of my grist with those, otherwise about 8 oz if I'm doing something "wheaty" with like 50% of those grains.
Hardware
10. As mentioned, I'm running the 120V 35L unit.
11. Stock plumbing underneath, with the T on the output of the pump, going either to the spigot or recirc arm (but I only every use spigot when cleaning/draining).
12. As mentioned, I use the top mash screen.
13. I use the full length recirc hose, and it's long enough to bend down 90-degrees and sit on the top mash screen with a length of about 4-5".
14. I have the HED (and have used this since I got the G4).
15. Pictures below, but generally a nice fit of the pump filter screen/HED that has a bit of a gap at the outer circumference when installed, but is tight when pulling it up out of the brew unit. Using feeler gauges, with the screen biased all the way to one side, I was able to measure 0.057" gap.
16. Pictures below, but an even better fit for the bottom screen on the malt pipe. Biased to one side, I measured 0.016" gap with feeler gauges.