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If you're pages are actually out of the index (homepage too?), have you looked at your robots.txt file to be sure that's not the cause of the problem?  The multiple 301s won't harm you.   Of the items you mentioned, your 2nd point could really gum up the works as far as indexing and I'd say you're better off having removed the rel=canonicals until you figure that issue out.  If that was your issue, I could certainly take a few months for google to get you back in the index. Some solid authority building  should be among your priorities at this time.

Good to know!

Rexjoec, It is considered duplicate content and the same holds true for www and non-www.  You can 301 forward the non-www to www and use rel=canonical to avoid the duplicate content issue with between http and https.