2004 - 2009 the light will come on every 5000 miles. OCI is 5000 miles per the Maintainence guide. Mine has come on every 5000 miles since new. Both 04 & 08.
I have never flushed my tranny in my 04, 124k miles now. Owners manual states the tranny fluid is "Lifetime" fluid and does not require a change. That doesn't mean it will hurt to change it. You don't know if it has been used for towing ect... But you must use the correct Toyota Fluid. I believe it is "WS" World Service Toyota fluid. There are a few threads on this forum with DYI instructions. Here is one from TACOMAWORLD forum but the aplications is the same to our 4Runners.
DIY: Full Flush for Automatic Transmission - Tacoma World Forums
Here is a good link from J.A.s (another forum member) website for a Brake fluid flush. If your brakes pads are good right now, I would not worry about it until the brakes need to be changed. Make sure to look for frozen caliper pistons. It is a common issue with 4th gens, and seems to be even worse for Rust belt vehicles.
Toyota 4Runner Brake Fluid Flush
Tons of great info on J.A.s site. Great write-ups on mods he has done too.
Top4Runners.com - Toyota 4Runner Informational Website
I have this link saved in every computer I use.
I have never had my fuel injectors "Cleaned". I do not feel in is necessary. You can Seafoam the engine which many members have stated makes a big improvement in mileage, starting, and smoothness of idle. I have never done it, but there people that swear by it. You can find a couple threads if you search the forum.
If you have the V6 it requires a spark plug change every 30k miles. Yours should be due if it was not done already. Takes an hour or less in your driveway, parking lot ect with basic hand tools.
I would change the gear oil in both Diffs, (if 4WD) and the transfer case. You have no way of knowing if it was done. At almost a 100k miles it is well overdue. Although you will not find a Maintainence interval in the book for it.
4WDs have 6 grease points, 3 per drive shaft. 2wds have none, the are sealed.
If you have a V6 it is one of the easiest oil changes you will ever do since the filters sits right up front on top of the engine. 5.5 QTs oil for V6. V8s I believe you have to drop the skid plate to get to the filter, I do on my 08 Sequoia and it is the biggest pain in the ASS oil change I have every done.
Check/Change your air filter.
Serpentine/Accessory drive belt??? May be time for a change. I changed mine to a Gatorback belt when the factory started squealing at start-up. $25-$30. Buddy and a beer in the Driveway 10-15 mins.
Good luck with your New to you 4Runner!!