[lorendarith]

And, in general, what's your favorite way to extract DNA for 1D?

Generally, any commercial kit for DNA extraction of your organism will produce sequenceable DNA. Also any traditional methods you find in molecular biology manuals with in-house buffers also work e.g. phenol-chloroform.
It only gets a bit more complicated if you want to enrich or only select for really loooooong reads, then you'd have to pick a suitable method which yields very HMW DNA like some protocols listed here https://www.protocols.io/groups/mini...-on-their-mind

Can't comment on your RNA questions though

[apredeus]

Thank you!

Can anybody comment on how reproducible are the methods used to measure the DNA concentration for long DNA fragments? I can't seem to get consistent results.

[nucacidhunter]

Qubit or any other flourometric method is fine. For high accuracy at least 3 ul of sample should be quantified 3 times and readings variation should be below %10. Higher variation indicates that DNA solution is non-homogeneous and needs proper mixing.