I got a 2003 Chevy Tracker 2 door 2wd automatic from my grandpa passing away...and i want to know if the parts from older trackers/sidekicks are the same because i want to make it 4wd 5 speed

Older as in back to 1999 there are alot of interchangeable parts.  Earlier models (1st gen trucks from '98 and earlier) had slightly different frames and A arms, the 2nd gen also have rack and pinion steering versus the earlier models which had steering gear boxes and they didn't run air actuators and air pumps to engage the front wheel drive (which was a 'more better' set-up).  I imagine a creative person could just slide a Samurai front axle and leaf springs under the front of the truck and then hang a Samurai transfer case behind the tranny, mount a steering gear box to the frame, add over the top steering, modify a couple of drive shafts and make it work.  Many others have done it.  

Or you might just pull the complete front IFS from another 2nd gen, weld the ring that engages the 4WD when the air actuator inflates (to by-pass all the wiring and air pump/weakness issues), add manual locking hubs and go that route if you are hell bent on making it a 4WD.  Changing it from an auto to a 5 speed might be more aggravating than putting a 4WD front axle under it.  You'll get into swapping the trucks computer, wiring and hanging a clutch pedal to boot.  I'm thinking the auto tranny will look pretty good to you in the long run, especially for the effort and money it would take to convert it to a manual when you start looking into it.

so a sami axle and trasfer case can be used? are the transmissions the same in the 98 and older? My cousin knows his stuff about the older ones...hes in the process of putting toyota axles on one of his, and has a samurai axle he was going to but on it

I know it can be done, others have done it (I have not).  If you use newer Sammy parts from 88.5 and newer model years the diff flanges will even mate up with the Tracker's.  You may end up having to use wheel spacers to push the tires and rims out from the suspension, but it is doable.  There is a difference in the frame widths you would have to factor in.  

Can't say for sure on the autos, but the M59 I have in my 2002 Tracker has interchangable parts (like the shifter tower) with 97 and 98 Tracker manual trannys.

Before you begin your project, I'd recommend you spend twenty or thirty hours perusing the search engine here on Zukiworld.  Try key words like:  SAS, or Sammy axles under Tracker, etc.  There are ALOT of guys and even gals on here who have modified their trucks many times over the years.  There are quite a few hard core builders here on this site and a couple others who have the skills, the imagination, tools, equipment and money (not to mention tremendous energy) and have performed incredible modifications on their vehicles.  Stuffing Audi engines in their 1st gen trucks, putting Toyota axles under their trucks, etc.  They are all willing to share information, their ideas as well as the problems they encountered while doing them and how they overcame the problem facing them.  First read a bit, then ask questions on those areas you do not understand or cannot find information on.  Half the fun of owning these trucks is talking to others who own them too and watching their progress when they post up a build on the site. The other half is driving them.  Be forewarned... these trucks become an addiction.