Jack R
In an oversimplified description - Portals are your world object constructions (walls, floors etc even static entities, as opposed to dynamic entities ) = how your level is divided up into parts which are rendered by the engine. The engine looks at your level at compile time and makes decisions about how it divides the level up - the result can be that in some areas you end up with more portals than in other areas = more portals = more polygons = lower fps.
You can copy areas of a map but as far as I am aware they can only be pasted back into the same map - i.e. if you copy and area of a map (to clipboard) and close the map the contents of the clipboard are lost. Unfortuneately what is required to keep the contents on the clipboard is for to have the ability to have more than one map open in the Editor at any one time so you can copy or cut from one map into another map. That is not currently possible. I have written previously regading this issue and its something TGC should look at for the future.
Your only other option if you have already created a very large map that you need to break up into smaller levels is to save your map multiple times with different names and then remove parts from each one to create a broken up version of your level into different smaller individual map files.
As you have quite rightly stated and discovered this then makes things rather difficult in as much as each of your smaller levels would then have a library which may consist of numerous items which are not needed to accompany each level and so being unremoveable from the library and compile folder. If all your maps are part of one game it wont matter as any library items cannot exist more than once in your game compile folder anyway as they would be overwritten unless the compile process were to name them for instance as say Tavor and Tavor1 in which case the entity would be duplicated unecessarilly.
You can see how working successfully and to best advantage with FPSC takes a little getting used to - you are now finding out something of the need for gaining an understanding of how it works and planning around that.
Do not despair - I have built very large and complex maps so know it can be done. You must be careful if using EA to build very large and complex maps and make backups of your levels, so that in the event that you get any permaent failure of a level due to its complexity - you can use an earlier backup to recover your hard work from.
To make a single wall transparent you could copy the files from any default single wall segment that you can find in the folders.
Rename your copies leaving the default ones intact. Dont use the originals but use your copies. You can use wall entities but segment walls are better for this situation. The best method of achieving transparency is to copy the default texture for the segment you are using, rename it and edit that in your paint program. You will need to give it an alpha channel if it does not have one. Fill the alpha channel with 50% balck for a 50% transparency. A fill of 100% black will make your wall 100% transparent or invisible. In the segment srcipt file go to the object visibilty settings part and enter the line (if it does not exist already) Transparency = 2 that should do it - this method should be guaranteed to work.
BULLSHOCK 2
2 minutes is not a long time to wait for a large level = The FPSC editor effectively does a full compile of your level for a test run each and every time you test run the level which is why it deletes it again on return to the editor - which again takes some time.
It is a well documented and uneccessary waste of time as most users would see it but thats the way it currently works.
I have asked for TGC to consider new methods of compile for future versions of FPSC and made some recommendations as to how I thought - both editor test run and final game compile could be considerably improved.
TGC I believe are considering this and many other improvements to FPSC that will help addresss concerns for numerous issues that are well documented and requested/suggested as improvements that could be made for FPSC and indeed some issues that have not yet been requested as far as i am aware.
The result could be that Post V1 FPSC could well be progressing to becoming an even better program with many further improvements and enhancements