David, first off, welcome ! I love magna’s , very underrated in my opinion.
On your FJR, Sven’s advice above is spot-on and something that really needs to be done ASAP if it has the OE CCT. Good job Sven! On the subframe, in my opinion your passengers aren’t in danger, the part that breaks is under the top box, if you pull the seats off and look back under the tail piece where the tail lights go you’ll see a couple of vertical struts and at the bottom of those is where it breaks. Take a look.
Now with that said the stiffy by itself will not prevent a broken subframe but it will prevent the piece’s like your top box, tail light and rear fender from littering the highway behind you. The only things that will prevent the subframe from breaking need to support the tab/tongue that extends out under the rear rack. Flexing of that tab/tongue is transferred through those struts you see by the taillights into the lower frame and causes the cracks.
At this point the only things that take the load off the tab and prevent it’s flexing are the Yamaha heavy aluminum rear rack which had it been oe standard we wouldn’t be talking about this, or you can also use the givi sr357 or the similar Shad tube rack, those are your choices. I have added the Yamaha aluminum rack to my 2014 after my subframe broke with a stuffy installed. It is the most expensive option.
Looking at your photo’s it looks like you have a Yamaha accessory top box from when your bike was new along with the accepted for that time mount, personally I would not run the top box until you get a different mount installed, just asking to break the subframe! Even empty, just the shaking of the box (25lbs) going down the road puts enough stress and movement into the rear tab that is transferred through the struts and into the lower subframe that cracks/breaks. I would not run the topbox in the current setup.
On the suspension, some of the more knowledgeable experts hopefully will be along and add their advice, but I’ll add that recommendations usually include using straight rate springs from suppliers like traxxion or racetech are better than the Progressive piece’s and a late model gen 3/3.5 model rear shock seems to be the “hot” setup for the earlier bikes. I used Racetech front springs and emulators on my 81 cbx and will say that it was a good transformation. I also used their seals & bushings that were supposed to be lower stiction piece’s, I’m happy with the very noticeable results.
As far as the seal leak you may try a Seal Mate tool which is basically a thin piece of plastic used to get under the seal lip to clear anything trapped there, you could make one from a piece of milk jug as well. Several here have had good results.
Magna's are very under rated for sure. I was on my way to a stage 3 build up which would have put just a smidge over 100rwhp, sadly I only touched the surface at stage 1 when my riding got sidelined. Was one of the funnest bikes I have ever had. If Dyna still made the ignition modules for it, I would pick another one up and start back over, it is KEY to making those motors run the way they should.
I couldn't think of the Racetech name, forgot about Traxxion as well. Appreciated, and I am definitely waiting for the "pro's" advice on what works. I hate doing things twice, and wasting money in the process. Being 15 years old and almost 300lbs, I'd just rather go ahead and upgrade at this point. Will make the handling crisper and braking superior to my weight load.
As for the seating/frame area. I will take some pics and post them back to you for you to see what is what. My daughter will lean all she can with that trunk on and I know it, she's all I have and we are pretty connected at the hip even all we've been through together
PLEASE KEEP THE INFO COMING!!!! And how can I change my screen name, I don't know how my actual name got used, not that it's a big deal, but still