Is the problem solved if I tell you that timers are unnecessary? See the rules here: www.speedrun.com/gtasa (click "show rules")

Try 3d analyze for windowed mode.

Fraps is used for recording raw gameplay footage (it just rips output from DirectX) however all the speedruns you've probably watched that use a timer use some sort of Scene based recording/streaming program. Most popular are XSplit (Paid) and OBS (Free). These allow you to build a "scene" that you record, so you can have the gameplay, timers, webcam etc etc in this scene.

For example here is my GTA:SA scene in XSplit, the game capture is only taking up some of the 16:9 scene, at the timer (and webcam which isn't plugged in so it shows an error) is taking up the rest, I'm free to just move those around as I wish.

So, you can either download OBS/XSplit and use that, or you can use fraps (which is a great program btw) and just record without a timer because it's the gameplay footage/evidence that is important, not the timer :P

Also don't use the windowed mod, it's a bad mod that breaks stuff and is also banned in speedrunning.

EDIT: We posted at the same time, yes what you said is fine, tbh your actually trying to follow the rules better than most other people (You read them) EDIT2: You show either the start of the game load, or comment the swimming times, don't need to do both but both is still fine :)