I installed 08 transmission on my 13 RK. Oil pan is different and I have problem installing mufflers (that is why I ride with gorgeous $7 flex pipes )
I have to switch oil pans or modify exhaust pipe under oil pan.

 

The 13 oil pan is a -99A part. It will fit. The tranny does not have to be removed, you can jack up the motor enough and pull the pan out over the crossover. It's a little tricky, but doable.

 

I assume you installed the '08 transmission as a unit; pan attached? You are correct that the pans are different; the '08 pan does not have the cut out for the under carriage cross over pipe. As Dawg says, the '13 pan will fit and if you have the OEM exhaust bracket that supports the exhaust system at the transmission and all the '13 OEM exhaust parts, your exhaust will mount as it should. I will warn you that the '08 pan baffle is held down by two pretty stout springs that must be dealt with to remove the pan; a true PITA, so gird yourself for a struggle particularly if you don't have a lift and must work off the garage floor. You will need something flat, thin and stiff to depress the springs as you slide the pan out. You will have to remove the rear wheel. You will not be able to remove the pan with a jack in place.

One way to skin the cat. Remove the pan bolts while the bike is on the side stand. Put the bike on the ATV jack and remove the rear wheel, pull out the pan. Install the '13 pan, put in any bolts you can while on the lift, maybe a couple at each end of the pan. Install the rear wheel, remove lift, install the rest of the bolts. The later pan has the baffle attached to the bottom of the pan; no springs to deal with. Installing an early model pan is a real PITA; worse than removing.

If your cross bar underneath the trans is bent, you will have to straighten it to remove the pan; don't use it a jack point. Having a small bottle jack handy to lift the motor/trans with the front motor mounts loosed may be of some assistance. I have been through this drill on my '02 FLHT when I converted the '02 exhaust to the later '09 cross under exhaust. I am so glad I didn't have to reinstall the '02 pan; the later pan just slips in place.

Like I said, a PITA but you will be a better man when the job is done and you will likely have expanded your vocabulary as well.