I see that they are in there, but I can't for the life of me find out how to make a magus, or gunslinger.
Okay, now that ENWorld seems to be back up I can reply.
Maybe I'm having a disconnect or not understanding what you are trying to convey. I'll walk through all the steps.
Note: I'm using v6.0.0 for my baseline.
1)
Download PCGen v6.0.0
1a) Also
download & install Java if you don't already have it (most likely you do.)
2) Start PCGen
3) On the Select Sources dialog, click the Advanced Tab
4) Change Game to Pathfinder RPG
5) There should be one of the following listings on the right side of the dialog
i) Paizo - Pathfinder Roleplaying Game Core Rulebook
ii) Pathfinder RPG for Players - Advanced
iii) Pathfinder RPG for Game Masters (includes Monsters)
If there isn't on the left select the Paizo menu listing and then scroll down till you find Paizo - Pathfinder Roleplaying Game Core Rulebook
6) Select that sourcebook, and either double-click or click the "Add Selected" button. It now should be on the right. This is the list of sourcebooks you will be loading.
7) In the pane on the left select the Paizo - Pathfinder Roleplaying Game Advanced Player's Guide and either double-click or click the "Add Selected" button.
8) Once those two (or more sources if you want), click on the "Load" in the lower right.
It runs through loading the sourcebooks selected then shows the basic info screen showing what is currently loaded.
9) Select "Create New Character", File > New or CTRL-N
10) Summary screen is the next one that shows, in the lower left is a pane called "Things to be Done" (which is new this version)
10a) Enter a name
10b) Select a race from the dropdown in the upper right
10c) Enter (or roll) for your stats
10d) Select a bonus language, if applicable
11) On the right where it says "Class and Level", click on the dropdown, and find Magus (or start typing Magus)
12) There is a plus sign below where it says "Add Levels" select that and you have a first level Magus, there will be more things in the lower left under "Theings to Do" each of those things is a link that you can click and it will take you to the tab that you need to be at to select the items listed.
I hope this clears everything up. If something shows up in red it means that you don't qualify. For everything but classes there's a pane in the lower left of that tab that will list the requirements needed, for classes you need to select the classes tab and then select the class.
