What is causing my problem with very low yields when isolating a 42kb yeast plasmid?
A dependable protocol for yeast DNA extraction I used to use was broadly similar to the protocols you cite but included an ethanol precipitation before and after the P:C extractions. The only expensive material was time. The general outline was:


Alkaline lysis
Ethanol precipitation
RNase A treatment of resuspended DNA for 15 minutes
Phenol:chloroform extraction (x2)
Ethanol precipitation


You probably know that the ethanol precipitation lore is that the yield is better the longer and colder you do your ethanol precipitations. I only ever did reverse transcriptase reactions a few times, but the template DNA I prepared spent the night in ethanol at -80C to maximize yield. Another place to double-check is that your yeast cultures are sufficiently dense before starting.