If you are unsure of the tuning a band uses in the song you wish to tab, I suggest listening to the entire riff. You can narrow down your tuning possibilities if open strings that are played during a series of chords or if a lead player plays some notes that pull-off to an open string.
Occasoinally the chords used by a band introduce slight dissonance, suspended intervals, or major/minor thirds/sixths. For example, when playing a maj7 chord, you play the tonic (1st) and the leading note (7th) at the same time, which sounds unstable. Chords with added 2nds and 4ths will sound colorful, as will the thirds and sixths in a chord or interval. The best way to develop your ear to tab harder chords is to play songs that you know or have music for and use these songs to learn what certain intervals sound like. When your ear becomes trained to two note intervals, it makes tabbing a chord sequence much easier, especially for jazz or classically-influenced chord phrasing. I also found a pitch interval trainer link on one of the threads on this site. For beginners, I suggest playing with the interval trainer first:
As for getting effects to sound like they do in the recording, this takes some patience. You need to first have a metronome or a watch to figure out the beats per minute (bpm) speed of the piece. If using a watch, just count beats by tapping your foot to the bass/drums/rhythm guitar and counting each tap for a minute (or a half minute if applicable). Usually an effect such as a tremelo or flanger will have a regeneration rate that is something like an exact multiple or 1/2 of the bpm in order to not sound out of place.
Currently my Schecter's Duncan Designed pickups sound fairly good through my tube amp, due to the nice gain and some EQ tweaks through the amp and my multieffect. I do want to get more sensitive pickups though for pinch harmonics and heavier distortion sounds, or possibly a replacement guitar. The pickup that come to mind is the Dimarzio D-Activator, or something similar like the X2N. Has anyone used these?
Let me know what you think of the pickups sound characteristics (compare to a famous guitarist's sound in a song, or something similar so I can understand more than your personal amp settings).
For Quick guitar parts, it especially helps to slow the playing speed in windows media player while transcribing from an mp3!
For solos, adjusting the panning control on the computer to Left speaker only (or right speaker only) will separate guitar parts if a band has a lead and rhythm part overlapping. It can be really tough otherwise, especially when the guitars play overlapping/counterpoint melody or harmonized passages.
Knowing scales and modes helps too. Try to figure out the major scale that your solo notes fall under, since the solo may be based from any note on the scale. This will help you know which notes would be played and in what frethand position the guitarist is playing on the neck.
If you have a question, send me a message or comment.