What's the difference betwen rot caused by phytophthora versus general poor drainage? Is it just cell death from lack of oxygen and not fungal at all?

A planting medium should always be made using ingredients of difference size. If bark is used, it should be 3/4 to 1 inch in size. Particle size is an important factor in selecting bark for a growth medium. The finer the particle size, the more the particles fit together and reduce aeration while increasing water hold capacity. In addition, finer particles decompose more quickly than more coarse particles. Perlite purchased in retail nurseries is really bad stuff. Pour some out of the bag an look at it. It ranges all the way from a few 1/4 inch pieces down to 1/8 inch then and all the way to almost the size of granulated sugar. When a range of SMALL particle sizes are present, the finer particles fit in among the larger particles and compact, again forming very poorly aerated conditions to the point of restricting water movement. When perlite and bark fines fill in the open spaces of the medium, it leaves few areas for needed air pockets. A good growth medium should contain between 30 to 50 percent aeration. Commercially, the number one growth medium used world wide is 3 parts bark, 1 part peat and 1 part graded 1/8 inch sand. Sand that is of a consistent particle size will not pack - Millet

Hmm... I did notice that the new brand perlite that I bought had a fair amount of smaller material in it compared with the last brand I used. The previous stuff had smaller materiel in it, but most of it was of a fairly consistent size (about pea sized). However, the medium didn't seem too packed when I de-potted the lemon, but I suppose it's a possibility.

I'll have to sift the perlite before I make a new batch and see if this problem ever repeats.

The worst perlite I have ever come across was sold by Schultz Lawn & Garden Company. Regrettably, Schultz is a nation wide supplier. - Millet

Haven't gotten Schultz. The old stuff I was using was NorCal perlite, and the new stuff was... I think Aztec? It was in a paper bag and I store it outdoors, so I ended up transferring it into the old bag (which is why I know what the previous brand was and not the new one).

Anyway, it looks like they don't have a screening for too fine perlite, just too large chunks. It's dusty enough that I wear a dust mask and goggles when working with it straight from the bag.

When I get large bags of horticultural grade perlite there are still some small particles that are sugar grain sized and smaller. I end up dumping the bag into a trash can that has 1/8" holes drilled into the sides and bottom and I rinse the perlite with water to try to wash the small stuff out. This perlite comes from a horticultural supply store in a 4 cu ft bag.

Millet is this why you no longer recommend perlite in potting mixes - because the perlite available is junk? It seems like a useful addition, I always wondered why it fell out of favor. Does seem to clog the root pruning holes in my air pot, though.