It's very easy to do all this on your own. Remember that these are major tourist highlights of the country, and Switzerland is justly famous for its efficiency, so they make it very easy to do.
For Mt. Rigi, you do a circular trip. You take a boat from Luzern to Vitznau; a train from Vitznau up to Rigi Kulm; a train back down to Rigi Kaltbad, a cable car down to Weggis, and (after a steep 10 minute walk downhill) a boat back to Luzern. If you don't want to do the steep walk, instead of heading to Weggis, head back to Vitznau. With a Swiss Pass, ALL of this is completely covered - no need to buy any extra tickets. All details of how to do this are in Rick's Switzerland book, including a train option from Luzern if you don't want to take boats at all (or want to go one way by train and the other way by boat). And don't worry about getting lost - lots of others will be making this trip with you, so you can always ask for help.
Going from Luzern to the Jungfrau area (the Berner Oberland) would be a long daytrip; you'll do much better to spend 2-3 nights here. This is also an important hedge against the weather; if you come for the day and the mountains are clouded over, you've wasted a lot of time (even if you have a Swiss Pass and so haven't spent extra money).
If you are staying in the Berner Oberland, it's again very easy to go up, on your own, for the best views. You just show your pass at the ticket window, and they will sell you a discounted ticket to the Schilthornbahn (with great views of the Jungfrau, Mönch, and Eiger - 50% discount with the Swiss Pass above Mürren, so your ticket is about 40 CHF) or the Jungfraujoch (in the "saddle" between the Jungfrau and the Mönch - 25% discount with the Swiss Pass above Wengen, so your ticket is about 125 CHF).
If you're daunted by these prices or don't have time for the longer excursions (or if the weather is iffy), you can take the Allmendhubel from Mürren. It's not nearly as high as the Schilthorn, but it's much cheaper (around 12 CHF round trip with a Swiss Pass) and you still get some great views of the three mountain peaks.
Remember, any trip that's completely covered by the Swiss Pass means you don't need to buy any tickets. You just get on the bus/boat/train/cable car, and show your pass when requested. You only need to buy tickets if something is not completely covered. You get a map with the pass; any route shown as a solid line is completely covered, any route with a dashed line is discounted. The map is available on line, but it's a bit hard to see unless you have a large computer screen.
