First thing I replaced on my Exe was the handlebar/stem.
1: my light mount would not fit next to the stem where I like it.
2: you can not roll the bars to your prefered position.
Plus, I managed to sell the bars for more than it cost to replace them :)
Somewhere on this forum amongst the 3000+ threads, someone has talked about this & mentioned a backpack that will carry a spare battery and also a top tube bag. You should be able to find it with a search.
I had a creak for a few weeks. Eventually cured it by removing fork & cleaning headset bearings of muck. The integrated headset cups are awful on this bike.
I had this with my 9.7 with a Fox shock. Trek replaced bike with an upgrade to same bike as you. No problem with this one even though it has those same chips.
2.8 😲 I fitted a Conti Kryptotal 2.6 and it barely fitted. Took it straight off as I didn't want to risk rubbing when cornering hard. Back to Maxxis Dissector 2.4
If you want to ride the bike without the main battery you are going to need an axs battery to change gear. I always carry one anyway in case I run out of main battery. You'll also need a ziptie or tape to hold the wire out of the way.