914 won't go above 3500 RPM

Did you re-calibrate your throttle position sensor?  It says you did in your post but if you did, I would think you would see 0-115% on throttle, NO?

If you moved or removed it during car overhaul, then yes, you will need too.

I can pull the bowls again and check. The 912/914 heavy maintenance manual says this about the bowl:

On 914 Series: Fix float chamber with the
attachment screw and O-ring 15.6x1.78.
Tightening torque 5.5 Nm (49 in. lb). Secure
with safety wiring.

But I doubt 8 in-lbs will change much. 

I did recalibrate the throttle position sensor and unfortunately, it didn't change anything. 

I thought the same, but the TLR instructions say a variance of +/- 3% is acceptable so I guess it's ok 

The float bowls are aluminum and bend easily.

Good Luck