You can start working on them but you obviously won't be able to trim the top or work on the ramps. You could do the sides and rivet on all the reinforcement parts.
You're going to need the baffles off to fit the cowling. If they were installed and untrimmed, you'd never be able to get the cowling fitting properly.
Once you have a nice cowling fit, hammer out the baffles.
If you really want to start the baffles now, just know that you'll need to fully uninstall them before cowl work.
No problem at all fitting them to the engine without the cowling - sure, you'll take them off again, but once you get used to it, that's a ten minute job, and they'll have to go on and off many times anyway.
I agree. Fitting the actual parts to the engine is not a long or difficult job (apart from a couple of pieces at the back, IIRC). The long and tedious job is trimming the top of the baffles to fit the cowl and that obviously can't be done until the cowl is complete.
It would be wonderful if someone would offer paper templates, or PDFs of templates that you could print and save those hours! Especially if they could be used on the individual pieces before assembly.