Yeah, the timer still counts. The only thing that stops it is the pause menu (not to be confused with the inventory).
It's a tactical restart. For example: at the start of 5-2 there are about 7 enemies outside of the spawn room. If you reset the checkpoint as soon as you spawn 2 of the enemies de-spawn. The only drawback is that you loose a certain amount of time depending on what version you're running. This can be done at a number of spots, but the only people who typically use these resets are NG Pro runners. Hope i helped :)
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Using a controller for steam is definitely optimal due to some of the tricks that you can do (C-Turning) and the precision that comes with it. I use a wired Xbox 360 controller.
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Using 'special costume 1', while not optimal, is fine. You will have to be a bit more careful, however. As for using mods - as long as it doesn't affect the gameplay in any way e.g. speed, item management, etc. it's completely fine.
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The game does have an IGT and that's how we judge a run's time. Splits are there for you to know how well you're doing.
Firstly, on 60Fps you can't do most of the important out of bounds glitches, loading times and inventory times are faster, and enemies are more aggressive. Second, we don't know exactly how much faster 60Fps is, but it is definitely faster than 30Fps.
I have never crashed on the door there. I think i've only crashed thrice; one was caused by AVG, and the other two were caused by an overload brought on by myself. So i guess there might be a way to prevent them, but if you're lucky, you won't get them often.
There's also this: http://pastebin.com/Scx6P0b5
if you don't mind reading a bit ^-^