I know that is on the form (which timer), but their standard punching puts all 3 sized holes on the track. Call or email Steve Monk for that.
Only you can decide what is best for you. If your real intent is for tuning cars, I would only get one lane. While two may look more cool, to me that is a lot of money that will be just sitting there most of the time. If you see measurable use running two cars, then great. Otherwise, most everyone that has a multi-lane track quickly picks a favored lane to tune on and sticks to it. I do care about resale, but you are going to put a lot of money out for that 2nd lane, so you really have to know that you are likely to get some use out of it. The second lane is MUCH cheaper to get new though than later, so keep that in mind.
Two stop sections, as others have said, without question.
If you are looking to save money on the timer, to me the choice is basically timer display or computer display. If you are OK with the computer display (and there are advantages both ways), then the hands down best for the money timer is the MicroWizard K1 cheap timer kit which comes with the serial option included for like $65. A little more if you don't want to solder. This only gives you lights on the track. Other choices I would go for are at least $200 though you could get their LCD timer discounted. Can't go wrong with any MicroWizard or The Judge brand timer stuff.
Length is a strong function of what you can fit. Again, if that last straight section is going to sit and collect dust, why worry about the resale ? If you have more room later there is a modest penalty for ordering that additional section later vs. originally - check it out yourself. It's not like the # of lanes question.
At the end of the day, BestTrack is pretty nice to work with. Feel free to call or email them to discuss, but remember, their perspective is Scout racing, not pro's, no many how many pros/leagues use their tracks.
