Chris,
No the engine doesn't have to be pulled. It's a cake walk for you based on your current modifications.
Check this thread out that i answered to: I'll get back to you tonight as stated in PM.
http://www.rswarrior.com/forums/topic.asp?TOPIC_ID=21669
Suggest you inspect spacer behind pulley for wear, pulley nut and of course the drive pulley splines and matting surfaces on all these parts. It's important that these parts tighten up perpendicular to the new middle shaft. You will need two new crush washers...one for pulley and one for final drive gear in transfer case. Transfer cover case gasket...one large gasket and small washer style gasket for center screw in transfer case. I pulled the transfer case and the pump as an assembly without any problem so no gasket required. You will need to pull your muffler to get at the transfer case. Oh....also will need differential fluid for reassembly. That's it for now