After a couple of failed attempts on the R and D box ( getting a bit messy now, but thats what its there for ), I installed it from source and got it running nicely at the first attempt. After mysqldumping from the old mysql 3.23.x version and plugging a load of holes in the documentation - I have all the mod_perl stuff happily working away.
The reason I upgraded was because I needed the BOOLEAN MODE full text support in MySQL 4.x and 4.04 seems pretty stable and reliable so far - haven't needed to recompile any perl modules or anything but ought to really at some point.
The search engine for $project now really rocks - total boolean support as well as a very very very fast lightweight application specific search that ensures that you get decent results for searches - by tuning the scoring and indexing in a way that simply isn't possible in a plan Database or Search Engine.
Now I just hope it stays stable, so far so good.