If i understand you right, your work is heavily based on the orchard-source. To keep the things simple you may just create a second remote for orchard (which only tracks the remote's master-branch) like this:
git remote add -t master orchard https://git01.codeplex.com/orchard
After that you're able to fetch or pull from that "new" remote. You may consider doing the "pulling in" from a special "integration"-branch to have more freedom within your master.
In this example I'm merging the 1.8.x
-branch into a integration branch:
$ git checkout -b integration
Switched to a new branch 'integration'
$ git pull -f orchard 1.8.x:integration
From https://git01.codeplex.com/orchard
+ 74136b6...37e9a33 1.8.x -> integration (forced update)
But be aware the normal merge will fail since your codebase can't be matched with orchard's codebase - they rely on different commit-ids. This is why you need to use the --force
-flag which disables the id-check and merges the stuff like hell.
After that - of course - you'll have a lot of merge-conflicts to solve.
To avoid the trouble with the merge-in in the future i'd recommend you to fork the orchard-repository and do the merge-in the other way round. Merge your project into the orchard-fork. Then you'll be able to rebase on future orchard-commits.