Open the project in eclipse, try to comment all suspect and error lines and tag them with a unique mark to find them back later. Try to get thru the wizard which does important changes in the java you don't want to do by hand.
After that look for obsolete jars and replace them with new ones.
Import all new modules from the appstore, but the wizard will do that for you. Only if the modules still gives errors.
Go thru all marked lines and try to re-enble them. Take the migration notes into account.
I found that if your userlib folder contains non jar files it also cause problems in this step. Make sure all sub folders and non jar files are removed so that the conversion can continue.
Did you try to do the conversion with the newest Mendix 5 version? Mendix 5.21.5? I have encountered some bugs with the older versions of Mendix 5 while converting.