[The Fifth Horseman]

Sorry, but not a newb error. Why? I do search for aliens, but it says no aliens were found and that the organisation did not the intrusion. It is not like the raid where you go in the building and got to handle the security guards. The alien infiltration was 19% and I had little to do so I wanted to kick their ass, but as I did not find them the organisation was not happy. Probably 19% isn't that much, but the building is next to portals and is already targeted like three times by those unmanned ufo's.

I drop in to check at the slightest sign of contamination. Can't be too cautious.
The aliens drop in on specific buildings and then spread from there, so in order to find them you need to crossreference the UFO trajectories from most recent intrusion with buildings owned by that company. Works 99% of the time.

Okay, first of all thanks for so much info.
I have seen many topics on this but tips tend to vary, which also leads to the second part of the reply to this.
If I do all these changes... what happens to my other simulated games? I have other games I run with DosBox, most noteably MoM and that is 200x320 resolution if I remember correctly. Won't that go screwy with these setting.
Also putting off sound emulation, won't that disable some sounds to be played in this or other games? If so I rather not touch it.
I might be annoying over this, but I rather have a dosbox working for all games that just focused on one.

This might sound a little complex, but there is a way of having several different DOSBox configurations, associated with specific shortcuts.
Go to Start menu/Programs/DOSBox. Right-click on the DOSBox shortcut and choose copy. Right-click on your desktop and choose Paste.
Now right-click the new shortcut and rename it to X-Com 3, then right-click it again and choose Properties.
Under Target, you'll have something like this (might differ slightly depending on where you installed DOSBox and what version it is):
"C:\Program Files\DOSBox-0.70\dosbox.exe" -conf "C:\Program Files\DOSBox-0.70\dosbox.conf"
The second part dictates which config file the shortcut uses. So change it to C:\Program Files\DOSBox-0.70\xcom3.conf , then go to DOSBox directory and create a copy of dosbox.conf, renaming it to xcom3.conf . Changes made to that config will not affect your main one, while you'll be able to run DOSBox under the altered configuration instantly by clicking the modified shortcut on your desktop.

On the not of Psyclone implants... can you use them on your soldiers actually? Reading the description I had hoped to get my soldiers with little bravery a bit boost in it due to different stimuli, but I can't seem to get it done (after all bravery is so hard to get up in X-Com (whichever version)).

Nope, Psyclones can only be sold for cash.

My soldiers with their poor accuracy start to shoot immediatly when they see the enemy through glass (like the poor AI) destroying the building, making tactics poor and stuff.

Give them sniper rifles, set them to kneeling position and fire mode to aimed. They won't shoot too often, but they'll hit most of the time and their accuracy will rise through the roof.

It is a bit of cheating doing that and I am not into cheating, trainers and the like.
I rather just go the normal way.

You may be interested in knowing that the game automatically reacts to such a massive increase in your score and sends out more and better equipped aliens against you.