Smelly, the u-shaped cowl that covers the powerhead mounting bolts has a seal that it sits on towards the bottom. You can see where it sits in pic3, it goes between the parallel ridges that are just above the painted area of the midsection.
That seal (like a large flat rubber ring) stops water coming up into the lower cowl. Ideally, if you can refit the seal around the lower cowl also it would be advisable but if you canot then perhaps leave it.
To get the lower cowl back into position just work it back and forth and side to side, after all, it dropped to that position in all your fiddling so it has to back to its original position also.
Of course, if you pull the powerhead off it will be easy to reset the lower cowl....... And it would have been a lot easier to have done the whole job....![]()
Cheers