Hello 4runner team, I am new to this forum and 4runner as well. Recently purchased a 2004 V6 RWD 4urnner with around 105k miles on it.
I'm having some mixed level of experience with this vehicle. Not sure how to describe the issue but here's what happens.

1. Morning cold start engine would make sound louder for first few minutes then calms down. I'm ok with that as long as it does not ask me to make morning coffee.

2. Main concern: When I am pulling the car and hit the gas pedal, the slower I try to take it off the more vibrating sensation and roughness I could feel in my feet when the gas pedal is pressed. This is more consistent till the speed of 45-50mph after that it seems to be fine.
Also, this issue seem to be varying from road to road but it does not sound smooth.

I've tried to put the car in Park and press the gas pedal very slightly to see if there's any issue. But It sounds fine that way.

I've had fair share of experience driving, Camary, Corolla, Lexus GS350. So, I know what is a smooth drive as far as sedans go. I am new to 4runner as in SUV and am not sure if this is the common trait of vibrating when you press the gas pedal or if something is at fault either in body or engine?

Any suggestion/tips would be appreciated. I hope I did not buy a lemon

Any suggestions?

It's louder when first started because it's idling high. That's normal. You can compare the idle speed first thing in the morning vs when you put it in park when you stop. It should idle higher after startup to get the engine up to operating temp faster.

Have you tried it in Neutral?

If you're feeling it in the pedal I think that would mean you're feeling the engine vibrating. If you can feel it while parked and in neutral, maybe have someone work the pedal or look at the engine while you do it so you can see if anything around the engine is loose or if the mounts are worn out.

It could also be internal to the engine. Bad spark plug(s) causing poor combustion?

If the vibration is the transmission slipping, I'd start with a fluid replacement using Toyota WS fluid. If the engine is vibrating, then take a look at the maintenance interval for spark plugs, air filter, engine mount failure, and signs of head gasket failure.

Good point on the transmission. If he has the 4 speed, I don't think the "rumble strip" issue is as common. But it's still possible.

Couldn't hurt to replace the fluid and maybe add some ShudderFixx like others have done.

OP - if you search rumble strip on this forum you should find plenty of threads about the torque converter slipping.

A 2004 V6 definitely has the 4 speed transmission, it can't hurt to do a fluid exchange on the transmission or several drain and fills over a month or two, it's much easier to do on the 4 speed since it has the dipstick since he can fill the transmission via the dipstick tube and much easier to check for the proper fluid level as well, he just need to use the proper fluid and not the WS fluid.

As far as the pedal, it has no mechanical connection to anything in the vehicle. It’s secured to the firewall by 2 10mm bolts and is connected to a large electrical harness. Try riding your foot on the brake pedal and see if you feel the same vibration while accelerating. If not, maybe check the bolts to see if they’re tight?

I tried that part of parking in neutral and slowly accelerate. I don't feel any vibration other than engine noise raising up with rpm going higher. I am new to his t4r but the previous owner (only owner) has good history on carfax for maintenance part.

Thanks for suggestions but it does not seem like Transmission is slipping as it would sound very harsh maybe? How easy is it to drain out transmission fluid on this truck?

The pedals seem to be secure. I actually took it today to the mechanic to seek his opinion. He asked me to sit on passenger side and took few rounds and asked me to raise my hand if I feel vibration under my feet on passenger side. I did notice it on few occasion on the passenger side as well while he was accelerating.
The mechanic then told me some 4runners has more some has less. Maybe enjoy the ride and if it still bothers you then bring it to me. Maybe he was being too casual as it was not a paid inspection. But it did leave me confused if there's a problem worth bothering or not.

I understand filling part but am trying to find some good videos to see how hard is it to drain and then fill transmission fluid.

Further looking at the carfax report it mentioned:

At 42000 miles in year 2010 -
Oil and filter changed
Power steering fluid flushed/changed Transmission fluid flushed
Emissions inspection performed

I am not really sure why would someone flush transmission fluid so early at 42k miles? Unless its being used to tow a lot that I think owner did not do.

So, if transmission fluid was flushed at 42k miles and given that right now its on 106k miles. Do I need to get the transmission fluid changed/flushed now?

How much intervals you guys suggest to do this process.

If you simply do a "drain and fill" it's really simple to do, remove the drain plug on the transmission pan, then replace it and refill approximately the same amount via the dipstick tube, drive the vehicle until you get it up to operating temperature and then check the fluid level with the dipstick making sure you haven't over filled the fluid level, if you have over filled it you need to drain some of it out, it's as bad to over fill a transmission as it is to run it low on fluid, doing a drain and fill you're only remove about 1/4 of the old fluid and you would want to do it 4 to 5 more times over the course of a few months and then you're good for 30,000 to 40,000 miles and do it again, just one word of caution be sure you're removing the correct drain plug and not the engine oil plug.

The second option is to do a complete fluid exchange and it's a bit more complicated, first do the same as a drain and fill and thusly replacing around 1/4 of the fluid, then there are 2 tubing lines coming from the transmission to the radiator you would have to disconnect the line that's pumping the fluid into the radiator from the transmission, (on the 5 speed it's the top line, not sure which it is on the 4 speed but as you proceed and if no fluid is coming out of the line you disconnected and it pumping out of the radiator instead it's the wrong line, reconnect it and use the other line), connect a clear piece of flexiable tubing to that line and it goes into a gallon or bigger jug, then start the engine and let it run until you pump the jug around 3/4 full, stop the engine and then add the same amount of new fluid via the dipstick tube, keep repeating this until you see the fluid coming out of the clear tube into the jug looks as clean as the new fluid, reconnect the transmission line to the radiator and check for leaks, drive it until it's up tooperating temperature and as above check the fluid level, again don't over fill it, you are done and good for another 50,000 miles or so and then do it again.

The third option is not a DIY job and that is to take it to the dealer or a very good transmission shop and have them do a complete transmission flush...if they have the proper machine to do it, just be sure they "DO" a complete fluid flush and not simply a drain and fill, some dealers will only do a drain and fill even when they say they did a complete flush and others will do the complete flush, also after dirving home or before if it's up to operating temperature, I would check the fluid level to be sure they filled it properly, if not take it back and have them correct the level.

Thanks for great tips and write up on the options to follow. I saw some videos and seem to be simple. But, I don't have proper mounts and somehow feel scared if 4200lbs weighing car could topple without mounting properly with all supports. I might take it to some reputed mechanic.

The owner last got the transmission flushed at 42k miles around 9 years back. Do you think it needs to be done now at 106k?

It's very good that the previous owner did get it flushed, I would still get it done again even if it's not causing the issue you originally post here, around 50,000 is what I would recommend as an interval, so if it were mine it would be overdo, others may have their own opinion on the interval.

Any lubricate no matter what kind it is will lose it's lubricating properties after a certain time frame, it's just common sense no matter what some manufacturers may say, such as Toyota saying the WS fluid for the 5 speeds being a "Lifetime" fluid.

That being said I don't have to raise my T4R to get under it to change the oil or transmission fluid, there's plenty of ground clearance to get under there without jacking it up, IMHO, if you have trouble getting under your's just just jacking it up a little bit to raise the body slightly but not even close to lifting the wheels off the ground should allow you more room.

If you choose to have some one else do this I would as stated take it to either the dealer or a reputable transmission shop instead of a normal garage, both should have the proper equiptment/machine to do the flush correctly, a gargae may not have the right equiptment to do it properly, but as I stated no matter who does it YOU need to do your own due deligence and check the fluid level after they have done the job.