I have a flac file (which can be converted to wav, if required) and its original cue sheet, is there any audio editor (freeware would be better) that allows me to adjust the start/stop position of the individual tracks from the cue sheet?
mp3DirectCut isn't precise; it's working on MP3 frame boundaries, typically in 1152-sample chunks with an unpredictable offset. (Precision is complicated by VBR, the bit reservoir, and encoder and decoder delay). mp3DirectCut then rounds down to the previous 588-sample CD sector boundary. Where this ends up being in the waveform is only close to where you wanted, at best.
The best visual cue sheet editor I've found (like, where you see the boundaries in a waveform view) is the free (for private use) CD ripping software Exact Audio Copy. In the program, after setting the WAV editor options to your liking, go to Tools > Process WAV, load the 16/44.1 WAV, CUE Sheet > Load CUE Sheet, make your adjustments, CUE Sheet > Save Cue Sheet. The saved cue sheet will have everything that was in the original except comments (lines starting with REM, which you may actually want, so some surgery may be required in a text editor).
Editing is visual but it's not the most intuitive interface; you have to leave the CUE Sheet Excerpt window open, double-click the track+index to edit, zoom in on the waveform with on-screen buttons (for X axis) and right-click-drag in the amplitude scale (for Y axis), and use the Set Time button to choose the new time (it'll round to a sector boundary automatically).
There's also the shareware wave splitter CD Wave (a.k.a. CD Wave Editor). File > Load cue sheet, make your adjustments, File > Save cue sheet. It can also generate split points based on silence detection. Operates strictly on sector boundaries. Drawbacks: no vertical zoom, writes very basic cue sheets (INDEX 01s only), loses most other info from loaded cue sheets.
And then there's the shareware wave editor GoldWave. It has features similar to CD Wave, plus a lot more unrelated functions. It has the same drawbacks as CD Wave. It also operates on sample boundaries, rounding to the nearest sector boundary (possibly forward) when saving the cue sheet.
Some wave editors, like Audacity, don't support cue sheets directly, but allow their internal markers to be exported to a file which is either in the cue sheet format or which can be converted to such with an external tool.
Personally, although EAC works pretty well, I prefer to use a general-purpose audio editor (Audition, Sound Forge, Audacity, whatever) to just zoom in on the waveform and get the exact sample positions where I want the boundaries to be. I then manually calculate the minutes:seconds:frames for the cue sheet from there (knowing that 44100 samples = 1 second = 75 frames), rounding down to the closest preceding frame boundary. I plug these into the cue sheet by hand, in a text editor, and test it by loading the cue sheet in EAC, ImgBurn, and foobar2000.
CueMaster can edit cue sheets. It can't preview them for you, however you can "preview" where to start and stop by listening to the file. If you need it to be very precise I would create a "crappy" mp3 file of it (to be deleted later) and use mp3directcut to find the precise timings. CueMaster and Mp3DirectCut are both free. I'm sorry I couldn't provide a better answer, but perhaps someone else here can :-)