adder - 9:10 am on Sep 4, 2012 (gmt 0)
Both sites are same niche and I just placed my Website A Link on Website B Home page
Do these sites offer a substantially unique user experience? If I search for "your niche" and then happen to visit your site A and then site B - will I have learned something new? if the answer is no, amalgamate both sites into one. Pick the stronger one and put all the effort into that site. Interlinking two sites that are the same niche and that Google knows are owned by the same person, is a very bad idea.
If you really need to interlink two of your sites, use nofollow attribute.
building back links for both websites from a same website
Not good. Definitely not good! It's only a matter of time before Google will establish a footprint. If you concentrate on one site per niche, you'll find that your budget goes further and you're able to attract better quality links.
If you have specific examples
I don't have specific examples but I have seen sites rank well using very popular (and very dull) wordpress themes. My main issue in the OP would be similar content and interlinking. Changing a theme on one of the sites wouldn't solve the issue in this case. They would still be considered manipulative.