I dont see how just lowering it colud make a bike ride rough, unless it is lowered to the point that the suspension is bottoming out or possibly lowering it to so much in the rear only that it changed the rake which I guess could change the way the bike steers and rides.

It seems to me that it is more likely that many people add lowering kits to their bikes and the rear shocks are already marginal, either stock or worse worn out stock shocks. So you combine the poor dampening and quality of the stock shocks with less travel and you have a worse ride.

On 2 of the 3 HD I have owned I replaced the shocks with Progressive Shocksand both times the ride improved. On my Sporty I changed to Progressive Shocks at 1000 miles and they were better than the stock shocks and now with my Fatboy I changed to Progressive 422s at 12,000 miles and lowered it 1" in the rear and it rides much beter solo or 2up.

 

smoother ride is the key....
how much you weigh?(this is where the girl beyotch slaps me....haha)
if your light, girls usually are...just adjust the preload of the shocks to a lighter weight which will cause a softer ride...
who knows, the previous owner might have been a fat ****....and had the shocks stiffened to the max....
if that don't work, see if a 98 has the same shocks as an 07....you can pick up a set of stock shocks on ebay cheap, with low miles, as that is usually the first thing peepz change...
here's a good website that explains about preloads...
http://fatbillscustoms.com/

good luck...

oh yea...I'm assuming that your a girl by your screen name...if not...SORRY

I lowered my bike in the front and the rear...I love it better than stock....but I ride a nightrain....just my opinion