I am working with a client to sumbit their site to directories. They intend to submit a bunch at first and then only a few every week or month when they have time. Will this work against them in the long run?
I don't think so. The number of directories you submitted will not bring google penalization, since the directories are not approved/rejected the same day.
Its not the number of directories you submit to that will hurt you, its the type of directory that will.
Avoid a lot of the directories as well, if you submit to thousands of them Google will soon see a pattern of backlink chasing and possibly penalize you. Work hard at getting natural links from non directory related sites.
Yes that is the best way. Hire a student and have them research similar sites to yours, contact them, and politely ask for a link.
It is of my own personal opinion and research/experience; that yes, it can. Acquiring too many backlinks too fast raises flags. I dunno what SE's algos have in place to check for this, but they surely do.