we've upgraded 5 or 8 dnn sites from ddn3 up to 5 over the past year, and they are each of them slightly different cases in the steps needed for upgrade and install of files. Mitchel Seller's information is the best around, and i've always followed the steps accordingly. Here are a couple of pointers that i'd share for the process:
- make sure to step up appropriatly... when moving far, like from 4.2 up to 4.9, move to 4.6 or 4.7 first... even then, afterwards you shoudl be able to go up to 4.9, but it's recommended to stop off at 4.8 first as the upgrade package of 4.9 (at least at one point earlier) was missing some key files. so, when in doubt, check on the files and possibly do a step between if you're trying to go too far in one upgrade step.
- those files take forever to FTP up and there are a range of reasons why one or two files can get missed in the overwrite process. any of the two or three times i've received the object reference not set to an instance of an object issue, it's been because of missing files or older versions mixed with new... simply starting from scratch and uploading the upgrade files again... even twice before starting the upgrade installwizard process can fix the problem sometimes
- there was on upgrade where the development.config file wasn't included or upgraded in the upgrade files, and a manual update of some of the lines in that file were necessary... that was around 4.7 if I remember correctly.