Definitely be very wary of sitewide links to your other websites. Google will not care if you own both sites and unless you have a strong backlink profile you will very likely be Penguinized.
One way to do it differently, and I have done this without a penalty so far, is to link a related page on site #2 to a related page on site #1, a different link for each page. In other words don't just link to the homepage of site #1 from all of site #2 pages. Link to many different internal related pages.