I have a similar problem with my cross cut sled with the weather and the seasons - one season it won't fit and 6 months later it barely touches the sides of the t-slot.
For the shelves - yeah I agree that the spacing is not that critical as long as both sides line up. I'd quite like to drill my track but it would make me nervous - my drill press is such a piece of crap too which doesn't help one bit, but the scrap with holes and a pin should do the trick I think.