A pre-plotted course/track on a GPS never works - too many obstacles, or construction, or other things.
It's been working OK for me. It's all about time. Doing points individually adds what, 30 seconds to each stop? I think I did 60 bonuses at last year's Minuteman. That is an extra 30 minutes. I do the entire route, and watch it carefully. I also print out a list of the bonuses, planned ETA for each bonus, and point value and put it in my map pocket to keep track of them, and gauge how I'm doing for time. But I'm getting ahead of myself.
I'm no pro, I've just done a few rallies but have done O.K. so far on most of them. I use Streets & Trips for all of my routing. I load in all the bonus locations then as others do, I change the pushpin color and/or shape depending on point value, whether there is a time limit (some require a business to be open, or daylight, etc.) Each rally uses a different point scale so each one requires different values when color coding.
Once I have them all coded I zoom back and just look at the map and see if any routes jump out at me. Not very scientific, but I can usually come up with nearly my final route within 10 minutes of looking at the map. I start by looking at the very high point bonuses and see how many I can connect together. Then I see how much extra time I have and try connecting the lower point locations that are close to that route. When I have S&T route I keep the speed setting (it is adjustable in S&T) in the center, or default position, because this most closely matches my riding. I keep my stops short and ride a bit aggressively, and this is usually pretty accurate. I have S&T auto-calculate the points I put in to see if it can do better than I did (it usually can) and then add up the points.
Next I try another route just using groups of bonuses that are close together. So far in nearly every rally, I have better luck avoiding the really big bonuses and going after many smaller point ones. With fast stops it makes more sense to grab four 3000 point bonuses than one 10,000 pointer even though that big bonus looks very tempting. The upside of this method is that if I mess up a bonus, I don't lose as many points. On the other hand, with 3-4x as many stops, it also gives me more chances to mess one up.
Read the rally book carefully!!! Look for wildcards and take advantage of all you can. Look for group bonuses- added points for getting certain bonuses together. These don't always work out to your advantage, but they can sometimes really add on the points.
As has been mentioned look for some bonuses near the end of the rally that use a lot of time but give few points, and consider those disposable. If you are running behind near the end of the rally, drop one or two of them to make up time. Have them planned in ahead of time, because you WILL make mistakes if you try to second guess yourself once you are tired. During the 2013 Minuteman I dropped a couple bonuses early in the day because I was a half hour behind schedule- bonuses I didn't plan on dropping. As it turns out I made up the time through the night, and finished the rally 15 minutes early without dropping any of my disposable stops. If I had gone for the ones I dropped it would have added 10 minutes to my ride, and given me enough points to win instead of taking 2nd.
Your best place to help yourself do well is to practice stops- both bonus stops and fuel stops. Take an old hand towel and write a number on it. Go for a ride and try to get off the bike, grab the towel, and take clear pics of it and another object. Can you access the towel quickly? If not, find another place to put it in the bike. Can you display it easily? Many of us use hangers or other items to hold the flag. A decent clamping hanger will hold the flag, and the hook comes in handy for hanging the flag at many stops. How about gas stops? You'll do a few during a 24 hour rally, can you do them quickly? Put your credit card where you can reach it easily. No need to burn through minutes just hunting for your wallet. Practice a fuel stop routine. Most of the top riders can fuel up in just a couple minutes. I've practiced a lot and can get off the highway and get back on with a full tank in 4 minutes. That includes exit ramp and entrance ramp. Why do a few seconds matter for a 24+ hour rally? I won't go into detail, but during last year's Cape Fear I was trying to make up just one minute so I would have time for a last wildcard bonus and it caused me to waste a lot more than that. I came in 8 minutes late and ruined what was possibly a winning route (if they were all approved I had the points, but was disqualified for being late).
As Dave said- the most important thing is to have fun. Rallies aren't for everyone, some just like riding easy and sniffing flowers. Nothing wrong with that, but it won't work for a rally. On the other hand, you will usually find yourself on some very cool roads, and each rally will leave you with interesting memories. Some of my best rally memories are riding back roads of Vermont in the middle of the night, all alone; winding down the hills & corners of the Lincoln Highway in PA during last year's Cape Fear; and NY farm country just across the border from CT during the Nutmeg 400.
Jim