Hey we're getting somewhere. I'm assuming ericw found some leaks. I loaded up the map in TB2 and the level in Quakespasm.

First off you want to run Quake with the +developer 1 command line option or type developer 1 in the console and then restart. Either way you will now see much more information in the console. You can dump the console to a txt file by typing condump in the console. Here are your missing keys and items:

Bonus item fell out of level at '1920.0 1856.0 230.0'
Bonus item fell out of level at '1700.0 1844.0 6.0'
Bonus item fell out of level at '2272.0 1952.0 222.0'
Bonus item fell out of level at '2132.0 2144.0 -186.0'
Bonus item fell out of level at '1684.0 2144.0 -186.0'

In TrenchBroom in the View menu select Camera > Move Camera to... and type in those coordinates above. You will then be "inside" the entity. In this case your keys and other items are too low to the ground or close to other items so they've fallen out of the level.

There are lights in your level. HOWEVER, you have a light key in the Worldspawn that is making the entire level lit at 200 regardless of your light entities. If you delete that key your lights will work.

The gold key up top I think is being pushed down into the world by the func_plat you are using.

The level is pretty nice. I hope you keep working on it. We're happy to help. 

Hey we're getting somewhere. I'm assuming ericw found some leaks. I loaded up the map in TB2 and the level in Quakespasm.

First off you want to run Quake with the +developer 1 command line option or type developer 1 in the console and then restart. Either way you will now see much more information in the console. You can dump the console to a txt file by typing condump in the console. Here are your missing keys and items:

Bonus item fell out of level at '1920.0 1856.0 230.0'
Bonus item fell out of level at '1700.0 1844.0 6.0'
Bonus item fell out of level at '2272.0 1952.0 222.0'
Bonus item fell out of level at '2132.0 2144.0 -186.0'
Bonus item fell out of level at '1684.0 2144.0 -186.0'

In TrenchBroom in the View menu select Camera > Move Camera to... and type in those coordinates above. You will then be "inside" the entity. In this case your keys and other items are too low to the ground or close to other items so they've fallen out of the level.

There are lights in your level. HOWEVER, you have a light key in the Worldspawn that is making the entire level lit at 200 regardless of your light entities. If you delete that key your lights will work.

The gold key up top I think is being pushed down into the world by the func_plat you are using.

The level is pretty nice. I hope you keep working on it. We're happy to help. 

The map works well on my end but I will keep in mind what you said.

I am still getting used to how Quake feels. I mean AD got me back into it (didn't even know Quake had a mapping community before that!) so I kinda designed my maps like I would design my Doom maps. I am still getting used to tougher individual enemies and the slower speed. 

Thanks for all your support, it works fine now! Some trouble with the key I so wanted to place under the moving platform, but otherwise – pretty smooth.

I love making levels, but rarely finish them :).

I was so used to leaks and light surfaces overload that I assumed that there's a trouble with the light by the default xD.

P.S. Now the map looks less embarassing : https://drive.google.com/open?id=1J7gSfXqR3umYRURJ6wUOBlLBBFJU7K9k

P.P.S. I must say it's really increadible work you're doing for Quake community. It's hard to belive that the tools are still being made. 

Glad this is working now. I have faith in this level. You should finish it.

SleepwalkR and ericw are doing a great job developing TrenchBroom and keeping us all mapping after 21 years... amazing. 

BTW, how much space should be left around items and monsters for them not to stuck / to appear?

Dogs in my level glued to the walls of their kennels (64x128x64) and some items don't respawn if placed too close to the walls or to the other items, but not always. Like, for example, armor and rockets goes fine together, but rockets and nails don't and niches are apparently very item-unfriendly.

This key, I was speeking about early, finally it got right where I want it, but it's like pure luck. 

All monsters are Shambler-sized in their collisions, to the best of my knowledge.

64 width, 64 height 88 tall -- says the engine source code. 

That can't be right, this fullbright box compiled just fine and didn't drop the enemy into the void with an enemy's hitbox- listed as 32x32x64 in Trenchbroom- a single unit away from the wall. Making it touch the wall still spawns it but it ends up stuck (an error is shown in the console when using developer 1), but even one unit is enough to leave it free to turn around and run. 

It might not be right. I don't work with the qbsp tools. There may be other factors in play than just what the engine says is the monster hull, which is hull->clip_mins: -32, -32, -24 to hull->clip_maxs: 32, 32, 64. 

There are two bounding box sizes: 32x32x56 and 64x64x88. There needs to be some space around and above them for the monsters to be able to move and not produce a warning (or for items not to fall out) - they must not touch a wall or ceiling, but they can be placed right on the ground. As Spud pointed out, a space as small as 1 unit can be enough. 

Vertical, have at least 1 unit of space above the heights below. 2 is recommended. The origin(center point) can be put exactly on the floor, though for monsters it is best to put 1 or 2 units above the floor at least to avoid potential position rounding errors sticking them through the floor (should be rare in newer editors).

Horizontal have at least 2 units of space beyond the sizes below.

Items are an effective 62 units tall. Items are 32x32x56 tall and get moved 6 units up on level start so that they can be "dropped" straught down to instantly put them on the floor and also check to see if they are below the floor and thus "fell out of level".

Monsters have 2 different collision hulls regardless of the bounding box sizes shown in Hammer/Worldcraft or other which negke mentioned above. The bounding box size for monsters shown in the editor should be close. Most smaller or narrower enemies use 32x32x56 (hull1), the larger enemies such as shamblers and vores use the 64x64x88 (hull2) size.
Dogs are a little wierd in that they have same size collision as shamblers, BUT...

There is a 4th layer of collisions...the qc code can define any bounding size it wants for an enemy. The engine rounds this size to the hull closest to either of the 2 enemy sizes for all collisions except raytracing and bullets. The qc lets, for unstance, giant monsters such as the gug, vermis, or boglord, get shot more easily in a way that is believable rather than only having bullets affect it right in the center 64units. Also tiny monsters such as fish or spiders don't get hurt if you shoot the empty air above or below them even though there could be 20-30 units of collision hull above these smaller enemies, shooting the air doesn't hurt them.

That is why, even though enemies appear to fit in niches in the editor and make sense from where you can shoot them, the tiny enemies still all need 57 units of vertical space. You can cheat it visually by using func_illusionary so long as the player can't reach the niche. 

That explains a lot. 

Also note that entities with bboxes will collide with each other according to their actual size, even though when colliding with BSP entities they snap to the two fixed sizes discussed above. Useful applications of this fact are left as an exercise... 

Do I need a different gbsp light and vis for Quake II or do the ones we use for q1 work? 

I think these are the most commonly used ones:
http://home.insightbb.com/~gryndehl/q2compile/quake2.html