You pulling the air shroud with the engine in the tractor? I don't think it was that big of an ordeal to pull the engine from mine. Had to remove a rat nest from mine. Take a good look at the driveshaft and its components while the engine is out. Won't be surprised if all your wear items are shot. I even had to replace the shaft on mine. Before you pour a ton of money in the engine price out what it would take to rebuild the driveshaft--anywhere from a few bucks to around $150.
I didn't bother the mufflers on mine, seemed fine to me. If memory serves me correct you'll notice one of them bolts on kind of crooked. Its behind the grill, your neighbors with green machines won't notice.
Seems they have an odd open end slot arrangement for bolting down with.
Oh yeah, snug up your steering box with the motor out, a lot easier this way. Don't get it too tight or it will be a bear to turn once you put the engine back in (don't ask how I know).