Quick Rhine Trip - opinions needed!

There is a direct regional express from Oberwesel at 5:33, getting you to FRA at 6:34. The next train is at 7:33 arriving FRA at 8:34 which would be cutting it awfully close.
Going down river is faster than up river. If you can stay in Braubach, take the 8:07 train to Ruedesheim and board the 9:15 K-D boat and go downriver to St Goar arriving at 10:55. Time to see the castle and get a train to Oberwesel for the afternoon.

You should be able to get a train from Brussels to Braubach with a 2 hour stopover in Cologne.
You can use point to point ticket ticket for Saturday 9/19. It is 12.10 euro to Ruedesheim, and St Goar to Oberwesel is a local VRM ticket for not much.
On Sunday, it is a 15.70 euro ticket to FRA.

However you arrange this, I would suggest you go from Bacharach to St. Goar, with the river. The trip from St. Goar to Bacharach, against the current, take almost 50% (30 min) longer, and there is not any more to see (Lorelei and Pfalzgrafenstein). 40 minutes is enough time.

"Am I missing anything I really need to see"

If you cruise from Bacharach to St. Goar you're only cruising half of the truly scenic part. Start in Bingen instead and you'll see a good bit more - Rheinstein Castle, Ehrenfels and the Mouse Tower, and more - in just 1.5 hours.

https://upload.wikimedia.org/wikipedia/commons/e/e3/Maeuseturm_Burg_Ehrenfels_Bingen_Rhein.jpg

YOUR PROBLEM IS FINDING A ROOM in a convenient spot on a very busy weekend at this point. And you need a base closer to FRA, preferably for 2 nights.

I suggest that you do this...

9/18: Leave Brussels early - around 7 am? - and with a 2-hr. stop in Cologne you can reach St. Goar by 2-3 pm. Drop bags at St Goar TI (open til 18:00.) See Rheinfels. Train to the Smarthotel in Ingelheim (has available single rooms w/ breakfast, as of now anyway, for the 18th and 19th, less than €100/night, not too far from Bingen to start the cruise.)

9/19: Take 8:50 train 10 minutes north to Bingen Rhein Stadt station for 9:30 cruise north. Stop over in Bacharach for 1-2 hours. Continue cruise north to St. Goarshausen. Do some wine tasting in the old city tower there if you want.
http://www.welterbe-atlas.de/uploads/pics/loreley-wein-und-heimatmuseum-st-goarshausen.JPG
http://www.rhein-lahn-kreis.de/images/refm/large/12/image_112.jpg?PHPSESSID=a8drmf97i8csskna69emou7dthn601h7

Take a train north (20 minutes) to Braubach for Marksburg tour. Return to Ingelheim by train later via Koblenz and Oberwesel.

You can use a Rheinland-Pfalz ticket (€24) for all the trains this day.

9/20: Leave Ingelheim by direct train to FRA at 6:47, arrive FRA 7:20.

I'm with Russ on this one. Your first priority is to find accommodation. This area is sold out months ahead of the Rhein in Flammen weekend. Unless you know where you have your bed, it's hard to build a workable itinerary beyond general recommendation such as taking the cruise with the flow of the river instead of going upstream.

Ok, so I did some checking and I found a bed at the youth hostel in Oberwesel. Given that I have found a bed to sleep in, what is my best path at this point?

Thank you all for the replies!

Sam has already outlined the Sunday morning troubles you have from Oberwesel to the airport; you'd also have a long walk down to the station from the cliffside hostel.

Suggest you do my plan for 9/18 but after St. Goar, have a nice meal there and take the train to Oberwesel, just 5 minutes south.

On 9/19 check out, grab your bags and take the 8:25 train south to Bingen and follow the rest of my plan from there for the day; after Marksburg, if it were me, I would want to be closer to FRA that night than Oberwesel is, so I'd catch a train down to Mainz for the night to be close to FRA (it's only 20-25 minutes by direct train with trains running all the time.) Check the IBIS hotel in Mainz for the 19th - it's only 1 block from the Mainz Römisches Theater train station (nearest one in Mainz to FRA) or check the Mainz hostel (south end of the Volkspark in Mainz, nice view of the river, excellent breakfast but not sure how early they serve) and in the morning walk to the MRT train station (probably a 20-min. walk) for the trip to FRA. There are other hotels near Mainz' main station if those don't work for you.

The main problem you'll have with this plan for 9/19 is your BAGGAGE. The Braubach TI will keep it for you (open Sunday 10-17:00) but I don't know if the Bacharach TI will - it's open Sunday 10-15:00 and you can try. Or you can email them in advance to find out.
info@rhein-nahe-touristik.de
If not, you'll need to schlepp it around while you sightsee in Bacharach. You can take your bags on the KD boat in Bingen. Staying 2 nights in Ingelheim or in Oberwesel would mean no schlepping at all (but Oberwesel has the transport problem on the 20th.)

Thanks Russ! One more question relating to your suggested itinerary. What time do the fireworks start that saturday? And how late into the night does the wine festival go on in Oberwesel? I'd hate to miss those things considering I'm going to be there anyway, but if things wind down shortly after the fireworks, I can see how getting my butt to Mainz is probably the best idea.

The last direct train to Mainz Saturday night is at 10:25 pm. Takes 58 minutes.

The fireworks that night are in St. Goar and St. Goarshausen... where did you read they're in Oberwesel? There's a fest in Oberwesel in the evening - but there's one in St. Goarshausen as well starting at 12 pm w/live music all day, fireworks from 21:00 to 21:45, music after that. Entrance fee of €5 includes a wine glass. You can see the fireworks from St. Goar as well of course. The same train Sam mentions leaves St. Goar at 22:19. If you get a room in Ingelheim, it will get there at 22:56. If you're going back to Oberwesel it's just 5 minutes.

Source:
http://www.loreley-touristik.de/veranstaltungen/rhein-in-flammen/