I love the Toomey as a good all-around pipe. My son raced with it all last year, now it is on my 94. Good quality pipe with easy installation and great instructions. Great sound, too.
Honestly, I have almost never used the stock carb, so the jet question is hard to answer, but it stands to reason that if they say to use it, that it will work. I do know that they say to move the needle clip from slot 3 to slot 2 which would lean out that jet a bit. (you can always put in a slightly smaller jet if you foul plugs) The filter is a UNI which you can't go wrong on. Personally I did away with the lid entirely, but if you ride through water at all then stick with the lid and vents.
All in all, yeah I would recommend it as a good kit and the only kit I know of that takes all aspects into consideration. There might be "better" pipes out there for racing or other specialized apps, but for a nice upgrade to a stock or mild blaster, I don't think you can go wrong with a Toomey.