Subdomains and root domains are not necessarily always owned by the same person and therefore will not always be given the same penalties. As Scott mentioned, they are seen as different sites.

e.g. If I create a new WordPress account and create me.wordpress.com and then build a black hat site which gets penalized, this is not going to affect you.wordpress.com or  www.wordpress.com.

Have a look at this article from matt Cutts

http://www.mattcutts.com/blog/how-many-links-per-page/

The original reason for the 100 link recommendation was due to technical limitations but this is no longer the case, 100 is still a general rule of thumb though. There are certainly times when you need to have more than 100 links, look at Google Plus for instance where the do what you describe above and load further content as the user scrolls down.

Keep in mind though that the amount of value each link can pass on depends on the total number of links on your page so you still wouldn't want to go crazy and link to every page on your website from each page. You mention that all links will not be included in the source code though so you shouldn't have the problem of over diluting the link value. Just make sure that all the links that appear when scrolling are included in a sitemap so they can be crawled.

No you shouldn't have to if you are building links naturally. What was your strategy for acquiring 200 links per day?

You don't, your IP address may be recorded by the site you have submitted the link to but not by Google.

However, if you are using proxies then you are probably doing something questionable in the first place and there is a chance you will get into trouble anyway. Especially if you are creating 200 links per day, they will notice this as it wouldn't look natural. It sounds like you may need to focus on a more natural link building strategy if you want your site to stay in the SERPS long term.

Did you read through all the comments? There is a lot of useful information in there. Here is another article by Rand shortly after the update that describes how this will affect websites:

http://www.seomoz.org/blog/google-says-yes-you-can-still-sculpt-pagerank-no-you-cant-do-it-with-nofollow

Here's a simplified example: Say you have a page with 10 links on it, this page is essentially passing on 10 points of Page Rank (PR) to other pages on your site. If you nofollow 3 of the links you are only passing on 7 points to the rest of your site, the remaining 3 points evaporate. If you have 500 pages on your site and you nofollow just 3 links on each page then how much of your PR are you wasting in total?

This is why Matt recommends that you let your PR flow freely through your site. PR sculpting using this strategy used to work before they made this change in 2009.

Of course this is still down to interpretation and how much you believe what Google says, obviously they don't give away too many secrets. This question gets asked in this forum every week and I would say the vast majority of the SEO experts here  advise against this practice.

I hope that helps

Todd is right, this won't save your PR from leaking. This strategy died years ago. Have a look at a similar topic here:

http://www.seomoz.org/q/duplicate-internal-links-on-page-any-benefit-to-nofollow

or here Matt Cutts describes how 'Page Rank Sculpting' no longer works:

http://www.mattcutts.com/blog/pagerank-sculpting/