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A couple people have pm'd me asking how I did the Mini-Rack mod. It has been covered, but not in this kind of detail, so I thought to post this to help those who needed some more clarification. It's actually quite simple once you start pulling screws out/the rack apart, but for those who are a little more OCD like myself, this might come in handy.

Get yourself a good Torx wrench (I got a multi wrench like the allen units that have all sorts of sizes-you'll need a fairly large one), and simply start unscrewing ALL of the hold down bolts (some are very tight)- some take a good yank. You'll need to remove the entire rack to do the mod. Once you've removed all bolts, be sure not to lose any of the metal clips (we'll get back to these clips later) and bolts that hold the rack down (in case you want to use the rack for future use). The rack can be lifted off by one person - it is aluminum and very light (I thought I'd need help but it was extremely light). Now you'll need to flip the rack upside down and unbolt all the spacer bolts/mini-towers that hold the top/bottom together. Again, these come off using a Torx wrench. The last part to undo are the two bolts (one on each side) that hold the rear feet to the rack-these, oddly enough, are allen screws (duh) and are accessed through either a circular or square hole under the foot. Loosen the cross bars so that you can now seperate the top rack apart and away.
Once you dismantle the top-half off, you'll need to rotate the rear H-shaped connector that hold the top/bottom rack units 90 degrees to the inside (facing forward). Some people drill in to the aluminum, but I think it's better to drill in to the plastic through the existing hole (it's also on the inside so it won't be seen this way :) ). Drill a hole through each existing hole so that you can re-use the screws that went in the hole originally. I drilled a little at an angle because it is hard to get to, but once the screw goes in, it's ok and levels out and tightens flat against the rack. Now throw the min-rack back on the truck.
You'll need to call your dealer to get the plastic white covers to cover up the front holes now left by taking the rack off. Whatever they say, all you really need is the white caps (about $10 each and can be purchased quickly from TRDSource in LA-talk to Mike, Dennis or Roberto). Remember those steel brackets? ...the u-shaped steel brackets off the rack that were in those openings to hold down the original rack (you can get new brackets, and the advantage is they come with a pad of neoprene to keep water from seeping in the screw holes, but you could make your own or add a drop of silicone-I didn't do anything except add the new brackets since they came with the little rubber pads). The dealer sent me new brackets and shorter screws. I'm not sure if the existing screws are too long (could be-you'll have to figure that oue out, but I know the screws they sent me were shorter and not Torx).
The rack is now at least 4" shorter and now I don't freak out everywhere I go, plus it looks great, still serves a purpose (even if only half a purpose :) ).
Hope this helps!
Here are some photos of the finished mod (sans covers-those came in a day after these pix were taken).

Additional pics for this type of modification:
All new Roof Rack Diet... Mine was a bit too big :( - IH8MUD™ Forums
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