As far as Google is concerned, you have removed all of the old URLs and have replaced them with new. Since all or most of the back-links to these URLs likely specify the old top-level domain, it will take some time to pass the PageRank for all of those old URLs through your 301 redirects, and to properly re-calculate the new URLs' PageRanks.

This is an entirely back-end process at Google, and certainly won't happen 'instantly' (as compared, say, to the immediate effect of a redirect showing in a browser). It will likely take several spidering/ranking cycles to normalize.

Reports here seem to vary, but range from a few weeks up to about a year for a site to 'settle down to normal' after all of its URLs have been changed. It depends on how often each and all pages are spidered, and how much Google 'trusted' the site -- Understand that you've given Google a bit of a shock by changing all of these URLs, and it may take a while to get its wits back again.

Spend however long this recovery takes getting backlinks to the new-TLD URLs and adding/updating on-topic content. As long as those 301s were implemented properly (I assume you verified the redirect Location and Status headers with an HTTP headers checker) and that each .com-TLD page redirects to the corresponding page on the .co.uk TLD, then there's not much else to do while you wait except to carry on with site development.

Whatever you do, don't 'give up' and revert .co.uk to .com -- If you do, the 'recovery clock' will simply start over.

Best,
Jim

Also, you're not losing traffic. Whenever the .com result gets a click-thru, the 301 kicks in.

301 come in two major flavours- internally, or cross-site. Cross-site 301s have been widely abused in the past, so now Google Trust-checks the URLs before passing the link juice, and updating the index.

As Google appears to be in the middle of an update, implementing 301 back-end changes may be low down their list of priorities and therefore have limited resources allocated to working them thru the system

The 301 re-directs are not tailored on a page by page basis, all of the internal pages on the .com domain 301 re-direct to the .co.uk home page because the websites URL structure has changed significantly.

I know its not ideal, but what we need to do is get rid of the OLD url structure, in exchange for the new URL structure, so we have redirected all the internal .com pages to the home page of the .co.uk website, now, there is no accessible .com pages, as they all 301 re-direct to the .co.uk site

Ah, thats your problem. 301s work best in a 1:1 relationship.

Your saying "content moved to here..." then when Google checks, its NOT there. Some other page is there instead.

Effectively, your new site is on its own, only with a head-start in terms of the PR that eventually gets transferred across. Old rankings will probably not transfer, although the old URLs will eventually get dropped from the index

Hi danielfoley22,

Did you use "Change of Address" feature of Webmaster Tools?

The Change of Address feature lets you notify Google when you are moving from one domain to another, enabling us to update our index faster and hopefully creating a smoother transition for your users.

You can read its details here:
[google.com...]