I'd look further than just that upgrade to find the problem. I have a G3 600MHZ 640 RAM iBook that seems to run a little faster after the upgrade.
I'm not sure what might be causing your slowdown, but the initial indexing can take several hours.
After the initial indexing, there shouldn't be a lot of processor time spent on new downloads unless they are many gigabytes in size. How big is your daily download?
The major indexing is only a 'one time' affair unless you add another drive. Initially it will cripple you, but then indexes on the fly. Check to see if you have Java 1.5 and I recommend using Preview to open all your PDFs, Acrobat or Reader can be slow especially to launch, which is not atypical of anything from Adobe