I bought a VP40 recoil spring and replaced the original vp9 recoil spring because the slide was very slow to go into battery when shooting unsuppressed. The 40 spring being stronger now causes FTE and stovepipes when shooting suppressed.  I switched back to the vp9 recoil spring and and malfunctions stop but brass barely makes it out of the gun.  How can I get cases to eject more positively?

Use higher velocity ammo.  What weight are you shooting?  There is a break in period.

I was using 115 bulk pack and mostly 147 Freedom Munitions.

There's your problem.

I've broken my VP9's in using Winchester 124 NATO, which is warmer than usual.

I shoot mostly 124gr FMJ (since my duty ammo is 124gr Speer Gold Dot) and some 115gr FMJ and haven't had any of those issues. Although, I don't shoot it suppressed and I maintain the factory VP9 recoil spring...

Doesn't matter if it trickles out or is thrown 20 feet the gun is running leave it be

I just got a vp9 and it comes with the .40 spring.  The first 100 sounds I used weak cci blazer brass 115 grain and had 2 stovepipes an alot of weak ejection.  Towards the end of the 100 rounds it was getting better.

I took it home and cleaned and lubed it, and also stored it overnight with the slide locked back.  After that I put 200 rounds of Winchester white box through it and it ran perfectly.  I even tried to make it malfunction by deliberately limp-wristing while using a one-handed grip, but it continued to work.

I think when you have the .40 spring there is a break-in period.  There was for me.  I would say shoot it some more and it should be fine.  

The VP9 is now my favorite centerfire pistol.