Obaraguy,
Clause 8.2.2 states:
"The organization shall conduct internal audits at planned intervals to determine whether the quality management system
a) conforms to the planned arrangements (see 7.1), to the requirements of this International Standard and to the quality management system requirements established by the organization, and
b) is effectively implemented and maintained"
I think the safest way to prove that you have determined that your QMS meets ALL the requirements of ISO 9001:2000 is to have audited all the elements.
If I were auditing a QMS & found that a part was not "effectively implemented and maintained" I would cite it as a nonconformity against the particular clause. My impression of the standard now is nonconformities found in clauses 4, 5 & 6 are normally more serious (system-wide) than those in 7 & 8 (usually more department-specific).
For the pre-assessment, don't worry too much if the auditors find that not all elements are implemented, that's part of what the pre-assessment is all about (though by now over 90% of the requirements should be met).
Incidentally, is the Registrar doing the pre-assessment or is it some other party?
Good Luck,
qualitymanager