Just one link per article. I create separate projects for inner pages - and only if they are worthy and will make me money.
Not all pages on a website warrant a SER project, or links for that matter.
If everything is very related I would probably take shortcuts so I wouldn't put a gun to my head.
Assuming everything is pretty related: I would try to do it in one project with multiple urls specified in the url box - each with their own specific set of anchors in that same box.
I would use the same generic niche article spin obviously with the standard anchor token. I would try to make sure the title of the articles was also more generic for the niche, meaning don't have blue widget in the title if you are also hawking green and purple widgets - just have 'widgets' - keep it more general.
I would probably do 3 a day for each url, so if it's 40 inner pages, then a submission limit of 120 per day.
After a couple of weeks I would lay down a Tier 2 mimicking everything in that Tier - just copy the project and make any necessary adjustments. And take it from there. Gradual escalation over the next weeks and months. You don't want to dwarf the importance of the main homepage so escalate as appropriate with that one.