The code upgrade tool is to be used for informational purposes even though it can "automatically" fix some of the reported issues. When you run the upgrade the majority (roughly 75%) of those 2000+ changes will be handled.
What I do is:
1. run the tool,
2. check the virtual objects back in,
3. take backup of the database and code,
4. run the upgrade (via KIM),
5. build the site,
6. fix errors to get site to a point where it will run and I can access Admin,
7. take a backup of the database and code
8. access Admin and checkout virtual objects,
9. build the site,
10. fix the errors,
11. check virtual objects back in,
12. run the site
13. take a backup of the database and code
Since there are a lot of API changes from 7 -> 8 this is needed. The instructions also mention the virtual objects won't be updated which is why all the checking in and out should happen.
It is a lot of work but if you don't have custom code or very little, it should take a short amount of time. I've got a site that's got a lot of custom code and is in ASPX (vs. portal) and have spent about 24 hours to upgrade from 6 -> 8.2 and still have a little time left.