Roof Rack
I'm not sure I can remember which mods came in which sequence. I practically lived on FJCruiserforum.com and took advantage of the collective wisdom and experience of many of the other owners there. Some have since sold their FJs, a few rarely post, and a couple have gotten banned. I feel like quite a few people there saved me some money and a few more saved me from doing something really stupid.
Perhaps the first mod was a Gobi rack. I called Gobi, not far away near Denver and arranged to have them install it. It didn't take very long, and I drive back home with my OEM rack stuffed inside the FJ. I sold it for half what I paid for it; a disturbing trend that would be repeated with a number of other TRD options.
Skid plate, control arms and track bar:
Similarly, the optional "skid plate" (AKA:"bling skid") was another $600 option that I was happy to sell for half that. Installing a Man-a-Fre skid made me worry less about driving off road. Over the years, that skid has held the entire weight of the vehicle. It's scratched and rusty, but without dent. Now, when jacking the front of the truck up to change tires, I'll just slide my floor jack under the skid and lift the entire front end. It's that beefy. Occasionally I think about getting alloy skids to save some weight, but I'm not there, yet.
With great effort, Man-a-Fre also supplied beefier upper and lower rear control arms. These should be easy bolt ons, although the drivers side upper control arm is next to the main gas tank, and is buried behind the auxiliary gas tank (more on this later). The lower control arms were an easy upgrade. Changing out the upper arms was complicated by the fact that Man-a-Fre's customer service has issues. They sent me the wrong control arms. Twice. Every call regarding the repeat mis-shipments started with something along the lines of "those FJs have lousy quality control, and there is a lot of variation in specs". Really? By three or four inches? The arms they kept sending were WAY too long. Eventually I got the proper arms, but had to remove a lot of stuff under the truck in order to get in and remove the old ones. It would have been easier if I'd done this in advance of other mods.
I had a similar experience with Man-a-Fre when trying to order a new track bar for the rear axle. This long link connects the rear axle with the frame, and helps keep the axle located while articulating. Three times, MAF sent me a bar 4 inches too short, and three times, they blamed it on Toyota. I bought a bar from TotalChaos.com; which bolted right in. I'm resolved to not do business with MAF again, until I see evidence of rational customer service. The place hasn't been the same since !Cruzer! Moved back to Oz.