snafu9t9, it seems you have a ~45k miles old fuel filter. it's due for replacement. get an OEM one from local or online dealer or WIX from Napa (Napa Gold). They last at least 30k miles, but other aftermarket fuel filters last ~15k miles tops.
here is a DIY on fuel injectors removal (5s-fe engine):
DIY Fuel rail & injectors removal - 4cyl i4 5s-fe gen4 camry - PICS !
I sent them for cleaning in California (RC Engineering), it cost me around $150 for all including shipping UPS 2 d day both ways, about a week turn around time (i'm in Jersey). they were only 72k miles old (10 years) and already out of balance (10%), after cleaning they are within less than 1% of balance.
New injectors cost (from online dealer) was $520 for just injectors.
If you don't want to touch them yet, Chevron Techron is a good injector cleaning stuff, but it won't solve dripping/restricted spray pattern problem if it's bad already. The RC shop puts them in chemical & ultrasonic bath, you can't do that yourself.
your tranny has nothing to do with it. computer controls fully engine speed in driving gears and will always try getting them into 700ish (norm is 700+/50rpm in Neutral gear, all accessories off). when Park gear causes RPM to go to like 800ish it's fine and normal, but anything above 900rpm in Park is NOT normal.
though you should drain/refill or flush it every 30k miles (including differential), that's what manual says. I did first flush at 60k at dealer as i was scared it's bad already (had some vibrations trouble like you do)
I think you can check vacuum ports on Throttle Body at idle to make sure you have zero vacuum reading from P & R ports confirming the throttle plate fully closes at idle. I don't remember which port exactly that was, but i can look it up, been there done that not long ago.
about your tune up items (plugs, wires and air/fuel filters). never use Bosch spark plug wires, if you have them, you can safely put them in garbage and get some decent OEM quality wires, like cheap japanese made NGK TE58 (~$40) from Advance Auto Parts or Amazon ($27) with free shipping. Bosch wires are horrible, i tried 3 sets and all of them were junk, they didn't last a month without some kind of a problem.
I don't think your Bosch+4 plugs are bad, but for future I could suggest sticking to Japanese NGK Laser Platinum or Iridium-IX plugs, this is great stuff!

those Bosch plugs tend to fail prematurely, for most people they do not last 30k miles as I heard.
is there any chance you can get a OBD2 scanner connected to your car and see live readings (fuel trims, MAP, o2 sensors, etc.) when engine idles ? this would be helpful to determine if your vibrations are somewhat related to what ECU does.
You can also try Sea Foam treatment in engine, tank and booster port (you will need to change oil after 50-100 miles). it can help smooth your car vibrations too if thats because of some dirt or carbon deposits.
EDIT:
NGK TE58 wires are for gen4 camry (yours is gen3), check here for gen3 camry wires:
http://www.ngksparkplugs.com/part_fi...uv/default.asp