Nothing wrong with using both.
Personally I wouldn't do it because I don't like changing the grip on my mouse all the time to keep my aim consistent.
Also makes it impossible to jump and shoot at the same time if you use m1 to shoot (unless you use space of course, but might be hard to switch fluently if you're used to using mwheel during fights).
But that's just me and if it doesn't bother you then just keep doing it like that.

Sorry, but I don't feel like that's good advice at all.
I'd say the opposite is the case. Small crosshair = more precision but easier to lose track of during fast flicks.
Big crosshair = less precision, but harder to lose track of.
For med/long range you need precision, but you don't have to do huger flicks.
For meat shot you don't need a lot of precision, since the guy is right in front of and will be a big target, but you need to do really fast swipes, because the guy can get behind or from one side of you to the other really fast, so you have turn around fast, which makes it more likely to lose track of your crosshair.
So a big crosshair is better for meat shots.
Also kinda gives you more time to react, since a big crosshair will touch the edge of the enemy player model slightly before it's center is on him.

So yeah, I'm a scout main and I feel like my overall aim is pretty decent.
When I play against good scouts in MGE, DM or PUGs I often feel like I can beat them 1v1 and at the start of the fight I'm often ahead, dealing more damage than I'm taking, thinking "yeah, I got this guy".
But as soon as they really start closing in on me to the point where you almost run into each other I lose the fight, because I tend to miss a lot of those important really close range shots, or at least more than the other guy.

I don't really know what it is.
I guess maybe I'm better at tracking than I am at flicking and meat shots require flicking, because the other player tends to go from one side of your screen to the other really fast.
I tried using a crosshair that pops out more and is harder to lose track of in those really fast motions.
Also tried to aim with my arm more so I can do wider swings with less effort.
Thought about changing my sensitivity, but I don't really want to mess with it, because like I said otherwise I'm kinda happy with my aim plus at about 9"(23cm)/360 I'm already towards the high end so I don't think it's too low to do fast flicks.
And if my sens was too high I guess mid-long range aim would be a bigger problem than meat shots.

So yeah, anyone got any ideas what I can do to get better at meat shots?

You say your aim isn't a big problem, but I'd say it's as least as much of a problem as your movement. There are multiple occasions in this clip where you miss 2 rockets in a row without the enemy even really moving. A lot of the times it looks like you are not actually trying to aim at all and just hit m1 as fast as possible. Try to be more patient with your rockets and wait for moments where your enemies movement is predictable for you.

But about your movement: I think your strafes are too small, you switch direction too often so your enemy basically only has to aim in the middle to get a lot of splash damage on you. Against shotguns this movement is Ok (still needs more variations), but against rockets the strafes need to be wider to avoid splash. Just wide enough to get out of splash radius but not too wide because that makes it easy to predict. Also try to use W and S a bit more. Way harder to predict than just A and D.

Thanks for this very in-dept answer. Really interesting, but I guess I'll live without it then ;)
Not nearly knowledgeable to make this work by myself.

Well if there is a real fix for this I'd like to know about it too, but from what Wiethoofd said, there isn't.
Plus I had this bug happen with a bunch of HUDs I've used and I assume that if there is a fix, the people that made the HUDs would know how to do it.

I have yet another question:
Under HudPlayerHealth there is the value "HealthDeathWarning" which is at 0.49 by default, so you're health will pulse red or whatever when you drop below 49% health.
You can change that value so that your health turns read at a different health percentage.
Now my question is is it possible to have multiple of those values and have them do different things?
Like at 75% your health turns yellow, at 50% orange and at 25% red?

I think this applies to your problem aswell:

It's really not hard at all to change the positions of ammo and health.
Just go to resource/ui and find hudplayerhealth and hudplayerammo and in those files find "PlayerStatusHealthValue", "AmmoInClip" "AmmoInReserve" and "AmmoNoClip" and under those titles find "xpos" and then play around with the values next to xpos.
Open the game, create a server, sv_cheats 1, change the files like described above, save the changes, then type hud_reloadsheme into console and the changes you just made should take effect right away.
This way it's a lot easier to find the right xpos values, since it's faster to change them multiple times until you got them right, because you don't have to restart your game multiple times.
And don't forget to change the xpos of the shadows accordingly (same files and names as above, just with shadow at the end. for example PlayerStatusHealthValueShadow for the shadow under PlayerStatusHealthValue).
Once you're done changing the white main numbers, remember by how much you changed the value and change the value of the shadow by the same amount. This way they have the right distance to the white text right away.

Whenever I join a new server my spectator HUD get's broken and I die instead of showing me how much HP the guy that killed me had left it shows %playername% or something.
It can be fixed quite easily with "hud_reloadsheme", but it's still kinda annoying.
Any way to fix this?

8.9 (22.6cm)/360
800 DPI, 2.3 in-game, raw_input 1

Scout main, some soldier and sniper.

It already is a VTF crosshair file.
At least there's one just like that included in the pack from the thread OP linked:
http://www.teamfortress.tv/35367/vtf-crosshair-pack

So you're using the VTF crosshair pack, which has the exact same crosshair you want included in it already...
How about you just use it then? ;)
Or am I getting you question wrong?

Am I just blind or is there no more min.mode customization file? In fact there are no more custom files at all any more? D:

Thanks! Will try that.

Edit: Tried to do what you said, but my problem now is that I can't find any color settings in there either.
Not really sure which part to change there or where to add the RGB code numbers.
All I can find are the "valueSpecgui FgColor " lines, but I guess those only change the colors while spectating.

I already had tried the first two and for some reason it didn't remove and didn't change it at all.
I'll try wide and tall later.
But the problem isn't just to remove the white cross but to get the numbers to change color instead.
I can't find a color setting for health colors, neither low nor buffer anywhere in the hud files.