I know I'm late to this party, but here's my twopennarth...
The D90 can be had, brand new, for £550 on ebay. If you can spring the exra few quid, it's a massive step up from the D40/60. In fact it's 3/4 of a D300, for half the price.
As regards tripods, you need to spend some money. The aluminium/plastic things from the likes of Jessops are a false economy. If you are on Albert Dock, and a car drives through New Brighton, the draught will make it shake like it's in detox. Brace yourself for a spend of £100+ on something half decent, plus extra for an adequate head. Anything less and you'll be wishing you hadn't bothered.
Re: Filters. If you buy them, buy the best you can afford. Sending the light through any more glass than necessary will help the image to deteriorate. Good filters are of the same grade as good lens glass, and so minimise any loss. Low grade filters are good scratch protection, but that's about it.
Karl, if it's not too late, rethink the 55-200mm. It's one of the weakest Nikon kit lenses. There are better alternatives for similar money.