I am about to combine an old site into another site. I will add the httacess file with 301 redirects. My question is will google count the incoming links from the old site to be incoming links on the new site.
in other words site A will be combined with site B. the old links to site A will now redirect to site B. Will the links old links redirecting from Site A count the same as a direct link to site B?
Oddly enough, almost a year ago today, there was an interview with Matt Cutts that asked that very question. He later clarified it in an email, but to quote:
Matt Cutts: That's a good question, and I am not 100 percent sure about the answer. I can certainly see how there could be some loss of PageRank. I am not 100 percent sure whether the crawling and indexing team has implemented that sort of natural PageRank decay, so I will have to go and check on that specific case. (Note: in a follow on email, Matt confirmed that this is in fact the case. There is some loss of PR through a 301).
The vast majority of link juice will be passed on to the new site when using a 301 redirect. Be careful that you do not have redirects pointing to redirects. Those redundant redirects will greatly decrease if not totally kill the link juice that is passed.
As youfoundjake mentioned Matt Cutts did say & later confirmed there is some loss with redirects so don't use them unless you have to.
It sounds like you are using the right solution for the right situation.