Ah yes... the dreaded bimini top-- bane of performance sailing everywhere! Ha-ha.
I took my aged main to the friendly neighborhood sailmaker and he replaced about 9 inches of bolt rope due to shrinkage. This had meant that the sail would never have pulled up to taut along the luff. This cost me $67. So I ordered a new mainsail cover from him too.
I would have the sailmaker come down to the boat (they all make 'boat calls' if you let them schedule it) and pull up the main to let him see it. Listen to his recommendations. If this is just not an option at all, then you pull it up, leave it stand alone, peaked, at the dock and take as many photos as you can. Then take him the sail and the photos. He will advise you about how much to cut off and on the issues of accommodating a bimini top in the first place.
Remember that trimming off the bottom of the main does 2 very bad things-- it reduces sail area at the biggest chord of the sail and raises the center of effort, thus imposing greater heel angle in less weather (the boat becomes more tipsy). Further, sailing with the bimini top up adds windage, weight, and uncontrollable sail area, and inhibits your ability to see and adjust sails, all of which are detriments to sailing performance which will detract from the experience of actually sailing.
About the only thing a bimini top improves is the experience of actually sitting in the sun, and you can wear hats for that when under way. (My dad used an umbrella clamped to the rail.) And being able to sail better when under way means you'll get to the mooring sooner, and it means have less time sitting in the sun while under way and more time sitting under the bimini top when moored.
Ask the friendly neighborhood sailmaker first.
