Your visa is your entry clearance. If you apply by post, apply 3-4 weeks before you want to leave. If you apply in person, you can theoretically apply the day before you fly.
As for being separated, no, you can't be separated for that long. Two years after you enter the country on your spousal visa (FLR/LLR), you'll have to apply for indefinite leave to remain (ILR). In order to qualify for ILR, you must prove that you've been living together as husband and wife for the previous two years (obviously you can be apart for trips/work, etc. for some of that time).