Git rebase/merge questions

    Recently i converted a very large CVS repository with a large
number of modules, branches and tags to Git as we have decided we're
going to migrate to Git.  At the same time there is some restructuring
that is going to be done.  We're actually splitting modules up into
separate Git repositories all together (not each module in it's own
repo, but grouping them a bit better).  Take these example CVS
modules:

Aproject1 Aproject2 Aproject3 Bproject1 Bproject2 Bproject3

They used to all be in the same repository but we're moving them into their own repositories:

git repo for A: Aproject1 Aproject2 Aproject3

git repo for B: Bproject1 Bproject2 Bproject3

And furthermore we're renaming them: git repo for A: xxx-project1 xxx-project2 xxx-project3

git repo for B: yyy-project1 yyy-project2 yyy-project3

There is also some other changes we're making that is more project specific (upgrading from Maven 1 to Maven 2). The plan has been:

1) create Git repo - note date/time
2) make rename/restructure changes
3) make build system updates (maven1->mave2)
4) copy all changes since step #1 from CVS into Git
5) cut over to Git completely

There are several active branches in place for each of these modules. For each branch we planned on executing those steps in that order. So what I initially did was step 1. Then step 2, 3 and 4 in "master". I then planned on merging these changes from master into each of the branches one at a time, effectively completing step 2 and 3 at once. This is where my problem lies. I've tried the following on the branches:

git rebase master this results in a TONS of conflicts (why would there be conflicts?)

git merge master same as above, TONS of conflicts

i've tried branching from master from the comment before i peformed
step #2 on it, removing everything but the ".git" directory, copying
everything from one of the branches (from another directory) into the
repo directory and rectifying the deltas by adding the differences and
new files and removing the removed files and then committing this
branch.  The theory being that it's a copy of master with all of the
changes from the other specific branch and then doing the rebase/merge
- still TONS of conflicts.

Most of the conflicts are (delete/modify) conflicts. I expected a few problems (10-20) but i'm getting hundred and thousands. Any help would be greatly appreciated!