All three of your questions have been the subject of NUMEROUS threads on this site. Use the 'Search' function and you will find all the answers you seek.
Welcome to the site and good luck with the shopping. You're doing the right thing by researching before purchase, which ever way you go.
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-Matt
2007 AT 4x4 Voodoo Blue FJ with MUCH
trail pin-striping
(As a former jeep owner, 1 cherokee, 1 wrangler) I closely compared both trucks before purchasing, and here I am with an FJ. My keypoints:
1. FJ had far more finish to it. The interior felt much more comfortable, and far better headroom (I'm 6'4). The Jeep has been choped a little since last year, and now i felt very cramped.
2. Smoother. Both are more than adequate offroad, but the FJ was so much smoother on road. You can actually talk on speaker-phone inside the FJ. As for engines, while comparable in HP, the FJ is a much smother reving engine, and the trans feels far more refined.
3. Didnt like how difficult the soft-top on the wrangler was. I didnt see myself actually going through the trouble that often to take it down, and the hard-top looks crazy without the whole thing off...a major project.
Alot of the perfomance and stats are very similar, but after test driving back to back, it was clear to me.
4. The FJ is something new. New style, more new technology, more headturning "what was that"-ness. I did go with silver which isnt to wild, but its an exciting vehicle none the less.
4. I am a little biased, because I have owned a wrangler before, but I was very ready for a quite/dry/comfortable/reliable vehicle, and I felt more confident thats what I would get with the Toyota.
Aftermarket is better (larger/cheaper) for the Jeep, but its coming along very
fast on the FJ, and most bases are already covered by many companies (bumpers, lifts, etc.), but still no companies like Quadratec. The issues you covered, winch and DRL bypass are no problem, and pretty easy mods.
Try them both, and go with your gut, because if you don't when that bill comes evermonth, your gotta be happy with what you got, if its gonna be worht it.
We were considering the same Jeep and FJ.....boy am I glad we got the FJ instead! Jeeps build quality has kinda gone down the tubes lately. Besides this is a Toyota...it will run forever! (Well, unless you get a lemon like Homedad...then you just get to turn it in for a newer model...it's almost like leasing!!)
I'm fresh with the FJ and traded off a 2007 Jeep Wrangler for it. Don't get me wrong, the Jeep Wrangler looks pretty rugged. But the FJ, I've found, is a whole new beast.
I agree with the previous thread, the ride quality is smooth in the FJ and, even though the Wrangler rides 10x better than the older one's, it doesn't compare with the FJ. The new Wrangler's already had quite a few recalls that I had to bring it in for, the weather stripping under the top wore quick, and the sixth gear didn't pack quite the punch that the FJ 6 has. You feel a lot more in charge in the FJ also, it reminded me of the Marine days, I feel like I'm in a tank!
if you have second thoughts of buying the fj because the jeep has 4 doors.then you prob won't be happy with the fj's 4 doors. so if you see what i mean the fj has 4 doors also. but the fj is a real offroading machine and will take you wherever you want to go. and I also see the fjc has less hangy down underneath side than most new jeeps i see. and I dunno if the jeep has atrac or not, but the fjc does and is a very impressive offroading machine. I cannot really truly compare the fjc to the jeep but i never even looked at one to buy. that close. sure the big o long 4 door version looks neat but one has to wonder if they really thought and tested them on the trail? and did they design them like they look just to stay in the market to keep them on the road? I am sure a jeep owner might chime in and set us straight. but i would never trade mine for one. hope this helps you a little.
I drove both just recently and there was really no comparison. FJ, hands down. Interior fit and finish was much better in the FJ IMHO. THe ride was good in both, but the Jeep felt seriously underpowered compared to the FJ. This was really surprising to me actually, but it was clearly the case. The FJ had impressive power, Jeep, not so much. It felt like it was always struggling.