7. What is the best way to download really huge (>100000 Kb)?

The short answer- this is hard on the web- here is a non web based solution.

The most efficient method is to find a file containing the sequence on the NCBI FTP site, preferably in binary asn1 format, download this file, and convert it to the desired format via the conversion tools at:

ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/cmdline/

If this is not possible, one may first download all of the components of the larger sequence. Then, using the information in the CONTIG field of the GenBank flatfile record, you can reassemble them to recreate the larger genomic sequence. To download the components, search for the NT_ record in Entrez Nucleotides then, select “Components” from under the “Links” menu on the right-hand side of the summary page. The components can then be displayed and saved in FASTA format or as a list of accession numbers or a gi list for later use in Batch Entrez. Clicking on the “Send to” button after selecting “File” from the neighboring pull-down menu will allow you to save the data locally.