@Dheej you sentence isn't too bad the adjective you want is 寂しい (さびしい) which means lonely, lonesome and can imply missing. so to change your sentence as little as possible you should write it:
personally i would not put the あなたは part in the sentence and leave it as just 僕が居なくて寂しいですか？ 'you' and 'i' are often left out in Japanese as they are implied by the context of the sentence. and since this is a closer person to you, i would leave off the ですか as well.
会いたい - is good for saying 'I want to meet you' with 'i miss you' being implied. 会いたかった is more like saying i wanted to meet you, with 'i missed you' implied. something you might say when you have met up again and you want to say you had wanted to meet.