Go for a 170mm airshaft, that'll help, on my Decoy I didn't have a height issue, but the extra travel gives added plushness (along with a Marzocchi Bomber coil shock, great mod!)
For sure, when I started E-biking, I got more pedal strikes than before mostly due to as Dax says, I was pedalling through terrain that I either would have ratcheted through or stopped........
Now, with 155 cranks and a more "aware" technique they are a rare occurence.......
If you'd lost almost all the air from the shock, the bike would be unrideable, for sure you'd notice it.
So you're probably losing air when you thread on the shock pump........
There's only a small volume of air in the shock and it doesn't take much to lose it