That Cat Stank . . .

Cake • It's called the American dream because you have to be asleep to believe it.
-- We found our male cat as a stray last year - just before winter hit. He's a sweetheart, but because he's not fixed (or declawed), he's developed some common behavior issues that unfixed male cats tend to get. Like him peeing and marking his territory on everything. 
-- We honestly weren't expecting to get a cat, so we didn't have any money saved up to get him his shots and get him fixed. We are saving up for it now (we have to get him his shots first - which are over $1,000), so it won't be an issue much longer. However, we are planning on getting a female cat after that's taken care of - one that's already fixed. 
-- But because he's been spraying the place up, our apartment has this horrid cat stank odor that I can't seem to get rid of fully. I don't wanna bring a new cat in to this scent-onslaught  (especially a female), so I'm wondering - how do I make my apartment smell nice and fresh again??? I've heard using baking soda, vinegar and water does the trick. Has anyone else tried that?  We just want our new cat to feel comfortable in her home :/ 
-- As a side note, yes, our male cat is just fine around other animals.