I believe when you are just coming to grips with a major lift, do the major lift as your routine, just drop the weight/reps as neccesary. Rack pulls, partials, etc., for me, are for guys who have hit close to a max limit and need a nudge over that limit. From what I am reading, I don't think you are at your limit. Not even close.
So, pick a day you yank hard, say Mondays. Then Wednesdays recover with light RDLs, or maybe no deads at all. Then Fridays do some stiff deads at 85%or so to complete the week and keep the back active and growing.
As for cleans, I'm with Swede. When you're learning them, do them first. They are technical and you should do them when you are freshest mentally and physically. The weights will be light, so they really are a GREAT warmup.
As you get better with them, it's a judgement call which comes first. I'm getting better at them, but honestly, if I pull some heavy deadlifts and then expect to try to clean some heavy weights, I'm more than bit fearful I will do myself a mischief. I still do them first every time. Static lifts are more brute force anyway. Cleans are very precise, and you can easily hurt yourself even with "light" weights, so don't disrespect them. At least in my opinion.
As for doing CLean and jerks, yeah, the cleans can replace deadlifts if that is your desire, but the jerk does not replace OH pressing. Maybe if you push pressed it (clean and press), but a true jerk motion does not fire the shoulders all that much. So, unless your goal is to be an olympic lifter, I would not do that in place of anything.
The goal of cleans is to fire up your fast twitch muscles to force them to help out your slow twitch (primary) muscles, so the overall muscle mass and CNS function are greater when you do your money lifts, in this case the deadlift.
So, what is your goal? A better deadlift means more deadlifting, plus adding in some cleans to fire up your fast twitch (power) muscles would likely help too.
On the other hand, if you just want to get olympic strong and efficient, do C+Js and Snatches and call it a day.