"Screw it! I came this far, why not become a complete woman?" Your clone says.
Wow, that was really easy, you are briefly troubled by the fact that you would so quickly give up your own manhood just for a chance to have sex with yourself. But that feeling quickly passes because you have a chance to have sex with yourself!
The two of you do some science type things in your workshop that culminate in the construction of a machine that can turn men into women. No big deal.
Anyways, it's finally time, the time you've all been waiting for, the entire reason you came to this site and clicked on those series of links and why you did all that reading and why I wasted my Friday afternoon to write this nonsense!
IT'S TIME TO TRANSFORM YOUR CLONE INTO A WOMAN AND THEN HAVE SEX WITH HER!
(wtf am I doing with my life?)
Your clone removes his clothes and gingerly steps into the machine that suspiciously resembled an 18th century torture device. (You had all these spikes lying around, might as well use them)
"You know, I think I might be having second thoughts..." Your clone says.
"Well, too bad." You say as you flip the switch.
All of your clone's body hair spontaneously falls off. You were expecting the spontaneous-hair-fall-off field to have more fan-fair and what not.
Suddenly a pair of suction cups descend from the ceiling and attach themselves to your clone's chest. Your clone tries to forget the fact that they were made out of toilet plungers as they suck his pectorals into nicely sized breasts.
A horrifying iron death mask comes down and smothers your clones face as it restructures his skull and skin into a more feminine shape.
Stacy, a local hair stylist that does home visits, walks over to the machine and makes your clone's hair look pretty. She seems to be kind of justifiably weirded out by the two of you but you tipped her a fifty before she left.
A series of pneumatic belts snake out from under the rig and wrap around your clone's body, they squeeze and crush your clone (in a process that you would imagine to be extremely painful) into a womanly shape.
A steel box comes up from between you're clone's legs and snaps around his genitals. There are some cutting noises and much screaming.
Then an artificially grown female reproductive system complete with functional synthetic ovaries is slided into the steel box which applies all the necessary fittings.
With a resounding beep, the machine snaps open and ejects your now sexy clone. The machine then proceeds to catch on fire. After dealing with that, you take a look at your shivering naked clone on the floor. He, uh, She now resembles what you would have looked like if you were born as a girl. Of course she is stunningly beautiful, you are you after all. She actually kinda looks like a younger version of your mom, or your sister if you happen to have one of those. Hot.
"It worked!" You cry.
"I'm a girl!" Your clone says.
"...These seem nice..." Your clone gropes her own breasts for a while.
Your clone slips an exploratory hand between her legs. "And this seems really nice!"
You watch sheepishly as your clone explores her new body.
Your clone casts a mischievous look at you and stands up. "Hey... why should I have all the fun?"
"Uh..." You stutter as you try to answer her rhetorical question.
"Come here." Your clone pulls you into your bedroom.