I'd imagine the safest thing to use to clean the pump internals would be diesel or kerosene...
Vaseline is fine, I've definitely seen others use it. I've heard the best thing to use is clean diesel though.
There's not really any way you can "mark" the timing with whiteout or whatever and have any hope of getting anything even remotely close to where it was timed before. The pump timing in particular is REALLY sensitive - a pencil line width is a big jump. I'm assuming since you have the pump off and since you've had a leak you're planning on replacing the timing belt at the same time too - it's probably diesel soaked, and as we all know diesel eats rubber. The new belt will end up needing a different amount of tension than the old one, also throwing off your marks.
You can get away without the tools and time it by ear well enough. Some people ONLY time by ear, some people use the gauge to get it close and go from there, some people just set it to what the book says and forget it. I think all are good methods, although the dial gauge gives you the ability to repeat your setting in the future, and allows you to know how much you moved things. You can make locking tools out of whatever you have around - I used to just use a socket for my pump lock, and I used to just do the cam by eye.