Some specific answers to your questions:
**Does it matter what order words appear in the title? Eg) Mens Blue Armani Jeans Jacket or Blue Armani Jeans Mens Jacket. **
Is it good practice or worthwhile to use seo titles with the colour of the item at the front?
Yes, the word order can make a difference, especially in a competitive niche. The question is, which keyword is a user searching for the product most likely to type in? Also remember the title tag is weighted with the first words earning the most weight. Do you feel "Mens" or "Blue" is the most searched for term? Or possibly "Armani"?
SEO title still, should I just include what that item is and nothing else?
Ideally you should focus a single keyword. The keyword is dependent on many factors. What keyword receives the most traffic? How competitive is each keyword? How relevant is your content to the keyword? How likely is that keyword to convert on your site?
Our meta descriptions are about 170-220 characters long for each item/page, is this too much?
Yes. They should be under 160 chars. http://www.seomoz.org/learn-seo/meta-description
Re: Duplicate Page Titles, you should use the canonical tag to identify the primary page. This tag will resolve the issue with the various sort orders. Also if you offer the same page via multiple URL paths, the canonical tag is your best means to resolve the duplicate content issue.
Re:Long URL, the meta description link above also discusses this issue. Keep them short and meaningful.
**Re:**No. of links per page, keeping under 100 links per page is a good rule of thumb. There are no hard and fast rules. Some sites could offer 80 links on a page and it could be too many, while another site could offer 150 links and it might not be enough. Understand your links control how PR flows throughout your site. If you provide a link to your best selling product and your worst selling product, you are telling Google these pages are equally important which is generally a bad idea. Try using category pages to reduce the links on any given page.
Rel Cononical: We have 2,591 of these. What are they, how can I fix it? It is important?
This question concerns me as it is more of a beginning SEO question. I strongly recommend reading the Beginner's Guide to SEO. It is a short and excellent guide which addresses most of your questions. The canonical tags do not necessarily need to be "fixed". It depends on how they are implemented.
Re:H1 tags, ideally each page should have one H1 tag which focuses on the keyword for the page.
Overall, my recommendation is to review the Beginner's Guide to SEO. Once you are done, examine your site and these questions and work through the guide again. At that point, you will need to decide whether to tackle these issues yourself or hire a SEO. Many of these issues are basic and you can work through them yourself. My concern is many of these topics would best be handled by a solid site design.
On the one hand, you can spend thousands of dollars addressing these issues. On the other hand, if you earned one more sale per day, you can increase your sales by thousands as well. The market is highly competitive. You need to earn a first page spot in rankings to truly perform well. The sites at the top often have professional developers and SEOs. It's entirely possible to do it yourself if you have the time and dedication.