Can you upgrade a ebox to a md5, I have a 5.3 with 930 cv's and am thinking about transplanting it into a baja bug that will see street use, and would like the 5th speed for mileage?
Will that use my current gearsets? and just add a fifth gear? Along with new shafts?

Yes, you can upgrade the "E" box to a "MD5"
Will that use my current gearsets? No, the "E" box runs VW style gears.The MD5 runs current MD4S size gearing.
The best bet is to sell the "E" box and build a new "MD5"
or use the case,diff,bellhousing,sidecover,driveflanges,and some internal conponents + about $4000.00 to upgrade yours.(see a dealer on that price)
Thank you for the question, call me if you have any other questions 619-710-8800 ext.110

Do you know if any of your dealers do trade in deals to say a s4 or a md4 or md5

Yes, some do. Call around and ask.

just put a freeway 4th in the e box and your done.