Here is what I would do assuming the MM is reused with no changes and assuming you have the red injectors
Go up to 98" with CP pistons and stock cylinders overbored, mild head work, compression at 9.9:1, Andrews 57n cam would be ideal. Goal would be close to or a little over 100hp and a big fat torque curve that comes on early. This will require changing all of the cam plate hardware including oil pump to 2007up big twin OEM parts available from the dealer. Andrews provides instructions for the conversion. Also needed will be the Andrews outer cam drive sprocket, details are in the instruction sheet. In the process of doing that the old tensioners will go away and the new hydra tensioners will take their place as well as a higher volume oil pump and roller chains front and rear. This cam plate assembles with slip together parts and no special tools are required. Nonetheless if you haven't built Harley motors before it may be wise to turn this over to a competent shop. At 65k I would be checking the rods which is easily done with the bottom end still together. Assuming the rods are OK and the crank runout is not excessive I would do a top end only build and ride on.
Use a Power Commander to tune it and find a shop that understands the MM.
None of this work and parts will cost a fortune but will restore the motor to as-new reliability and add over 25% torque and horsepower