It's been about 15 years since I made music.   Back in those days I would make my songs strictly out of MIDI using RealityGM or CHAOS Soundfont libraries.  
Over the past 15 years I've slowly collected a variety of instruments, VSTs, Plugins for FLStudio and samples.   Now that Im finally making music again (with horrible chord theory now  ) I'm noticing my sound quality is better and much louder using these Plugins and VST.   Everything except MIDI.

How can I boost the sound of MIDI samples in FLStudio or boost the sound of my whole song in post production without distorting or ruining anything?    Any feedback on the songs is welcome too.   You can be harsh.

Here are examples of what I'm making today.  Notice the sound is at a decent level that matches most streaming services.  These are using 85% VST and samples.   Most of my volumes are 25 - 50%.
https://soundcloud.com/tashawn-nicholas/clashing_draft?in=tashawn-nicholas/sets/me

https://soundcloud.com/tashawn-nicholas/relay-point?in=tashawn-nicholas/sets/me

https://soundcloud.com/tashawn-nicholas/d03?in=tashawn-nicholas/sets/me

Now here is my trouble song.   Its lead instrument is a MIDI instrument.  It is RealityGM flute.   Its volume is MAXED.   All of my other instruments are around 10 - 15% volume.   If they get any louder they drown out the lead instrument.
https://soundcloud.com/tashawn-nicholas/pipes?in=tashawn-nicholas/sets/me

NOTE: These differences in volume mostly show themselves in car speaker systems and headphones.  Not so much on laptop speakers or standard PC speakers.

There are several ways you can do this: 

1 Gain Staging: Make your VST tracks much softer to where they align with the volume of your MIDI instruments. Then on your mastering bus use compressors, maximizers and limiters to bring that overall mix up to an appropriate broadcast level. 

2) Create a MIDI bus that has some gain plug ins as well as limiters on it so you don't distort anything. Raise the level up to match your other instruments. 

Are you routing things from instrument families to aux busses and then working with those sliders? I've found this method works really well and you can add EQ/compressor and other FX to families on top of making individual tweaks on certain tracks. 

If something is peaking out then you need to work on your routing and signal flow so you can make sure nothing gets distorted. For example, if your limiter is having to do a ton of GR then you've got too hot of input signal coming into that plugin. Adjust things as you can and make a better balanced mix. 

Edit: Listening to your actual problem song. The flute part has some notes and hard attacks at different parts. A compressor (or a few of them) should really help bring down these harsh attacks while letting the software elements sit better in the mix. 

Some VST plugins are SUPER loud out of the box. For example, Omnisphere! I'm always having to turn that one down by about 15dB or so (sometimes more) just to make it sit somewhere near the mix. Other VST are much better balanced. 

Whoa thats a lot of info.   

So Im going to look up some tutorials on routing my midi through aux busses.  In FLstudio, I just take the SoundFont file from y library and place it into the track sequencer as a new instrument.   FLStudio just does the rest of identifying it, listing its patches and plugin features.   But I guess I could load up a VST then load the MIDI into that VST, if its designed to do that?

All you'd need to do is set up the output of the MIDI track in question. I don't use FL Studio however, so I can't speak directly to that process but I've used this same approach with Pro Tools, Logic, Cubase and several other DAWs. 

Thanks for the help.   Ill let you know what my results are in a few days I guess.