My view is that it's not worth the time unless the disc is of special importance, i.e. you can't get the content on CD. I prefer to put my time and effort into a high quality sound system. I normally keep away from MP3 unless it's for emailing demos. I doubt that you'd notice the differences between different software packages on ION vinyl transfers.
I do vinyl transfer professionally occasionally for reissues when the master tape has been lost. For the best results you need the best Turntable/Pickup/A-D convertor you can afford. I haven't listened to the ION but it's price doesn'tsugest audiophile quality. I use an EMT turntable with a Stanton pickup. The EMT has a built in A-D convertor and outputs SPDIF, which goes directly into the M-Audio soundcard. a combination worth more than 10 times the price. I use Sound Forge for cleaning the sound up. I admit that Cedar would probably give better results but I can't justify the price for the ammount of work I have to put through it.
In general Vinyl is usually always clicky. Only once in 30 years as a professional have I come accross a click free LP, which unfortunately was only of intrest to the owner because of it's sentimental value.