I used to install these for a living years back and recently added a new remote and changed programming on the old Python remote start I found that was installed in my 97 SR5 before I bought it. I have some experience.
I would recommend a 2-way remote start system with as long range as possible. Reason being is that you will know your truck is running without even needing to worry about it. Mine is one way and I'm always curious if it started or not....but I dont feel like spending the money to upgrade. You shouldn't have tore the old one out! It's MUCH cheaper to program a new set of remotes, unless it was just an alarm and not remote start capable.
The key on my 97 doesn't have a chip, so there is no need for a transponder bypass. I'm not sure they have one in 2000 but a local installer can tell you or a lengthy search will give you the correct answers. Some brands (usually the newer ones) have an ignition transponder chip inside the key itself and those need to be bypassed...but I'm guessing you knew that already.
Can you install it yourself? Are you capable of wiring some relays, diodes, negative trigger locks or horns? If you can't answer those questions with confidence then let a pro install it. Trust me it's worth the extra dough. You don't want to accidentally leave yourself stranded in Alaska.
Good luck and if you have any questions just ask! (I'm going to search and see if you need a bypass and get back to you)
EDIT:
Ok after searching around, I don't think you need a bypass. BUT you need to verify that by getting a spare key made and trying it out on your vehicle. Any hardware store can do it. Make a key and try to start your car. If it doesn't start...there is a chip....if it does then your 4runner doesn't have a chip and you are good to go!
Source Transponder List