Alignment tools simply consist of a feeler gauge that allows measurements to 1000's of an inch and the appropriately sized wrenches for the nuts on the engine mounts, oh yeah, and lots of patience.
If you've not had much experience working on a marine engines (I'm guessing from your question) in confined spaces both the trans removal/reinstall and re-alignment process may be pretty big jobs for a beginning DIY'er. Both also would be much easier with two people.
I'm sure you could find a number of books that describe the processes in detail. I'd start with the service manual for your engine. A Yanmar deal should have that. In FL, I happen to live near Mastry (
http://www.mastry.com/) so that is where I got my manual.
Brian