I think what happened was after I took the bike home from the shop (where it felt fine and was adjusted properly), I replaced the stock seat with one I already had and just set it up like my old bike, without realizing it.
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I stole this from another forum, but here is the hierarchy of Shimano systems.
ROAD BIKE PARTS.
LEVEL 1 (entry level)
SIS.
SORA.
SIS is not found on many road bikes now. However Sora is extremely popular. Many general commuting and entry level road bikes will be Sora equipped. Sora has STI levers and a very reliable gear and braking system, without being too pricey. Sora is a 8 speed group set and will come on bicyles ranged between $700-$1200.
LEVEL 2
Tiagra.
Tiagra is the first road group set that is 9 speed. Tiagra is used a lot by road cyclists that want the reliablity and smoothness of 9 speed without the price tag.
LEVEL 3
105.
This is a very commonly used component set a lot of top road bikes and training bikes will be equipped with 105 as it is exceptionally smooth in its changes and a very durable and reliable group set. 105 is also a 9 speed group set and its body predominantly made of alloy, thus making it very light. People who want good stuff that will last this is it.
LEVEL 4
ULTEGRA.
Once again used a lot for top end racing. Not often used for training bikes, however it is durable enough to do so. Very smooth and very light on its actions. This means changes with little effort.
LEVEL 5
DURA ACE.
The top of the line. Fairly expensive for the general rider.Dura Ace has been converted into a 10 speed system, with massive changes to the levers and crank sets, both so much smoother and lighter to use.
The above generally holds true, except for the thing about gearing.