I'm looking at a 2001 Tracker as a project.
 It has the 2.5v6 and auto so from what i read, it should have 4.875 gears.

Is there anyway to get 3.73 or even 4.10 gears for the 99+ Trackers? I want to get better mileage also.

If all goes as planned my project will be cruising at 80mph on the highway at 3500rpm if I have to keep the 4.875 gears... so I'd like to change them to lower my rpms down.

I think the highest you'll find is 4.30:1 - from the manual transmission Grand Vitara.

You also need to remember these engines were designed to produce their power at relatively high rpms, if you're not compensating for the gearing change elsewhere the possibility exists that you could drop the rpms low enough that the engine is out of it's power band, if that happens it will not only hurt the acceleration, it will kill the fuel efficiency.

My project will be a 5.3/4th from a Silverado. 

When I asked about the gearing, they made a list of 3.73 vs 4.875 specifically for that combo and at 80mph it was 3500rpm in OD with the 4.87 gears

I'm going to have to assume that translates to swapping a 5.3 litre engine in - if that's the case, you can ignore my previous comment on the engine's power band, in the absence of that little detail I assumed you would be running the 2.5 litre V6 mentioned in the original post.

Having said that, you need to recognize that the gears that would have been available for a Silverado, will not necessarily be available for a Tracker, GM would have offered higher gears to go with the larger engine, and those gears do not fit the axles on the Tracker - Suzuki (who built the Tracker) would have offered a range of gears to suit their engines - to the best of my knowledge the highest ratio you will get to fit that axle is the 4.30:1.

Off the top of my head the available OE gears are 4.30:1, 4.62:1, 4.875:1 & 5.125:1, aftermarket gears may be available but they are lower than you're looking for - I believe 5.7 & 5.8

4.30 would still be better then 4.875

Someone suggested maybe Samuri axles? They thought they had 3.73 in them. I don't know how much difference in size and fitment would be though.

I have no idea what gears the Samurais had, but the axles are not suitable for use under a 99 Tracker, and I suspect the 5.3 litre V8 would snap them like matchsticks.

LOL probably, but I didn't know if there were upgraded axles or differentials that would fit.

You could do a few things to make them better, but unless your going to be on-road only Sammy axles will probably always be a bit light for a V8. 

I never go offroad. :/

The donor I bought ended up having a 4.3 V6 so I'm thinking about keeping that and swapping it into the 01 4dr I plan on getting.

I figure it will fit better and still be more than enough power especially with a ECM tune and a vette servo in the trans.

For a road rig you should be ok if you wanted to go with a Sammy swap, but a Toyota swap would be better.  Centered rear axle to match yours and the width is closer to stock.

That's the info I'm looking for!
What Toyota would I be looking for, for axle donors?

its difficult mate
  jim

I've been in Mexico on a work sponsored trip, so haven't been online for a while. 

For Toyota axles it gets interesting.  Pre 84 you can get a front and rear axle that match, but most people use an earlier front axle with IFS hubs to widen it up then use an IFS rear axle.  There is a lot of mixing and matching of third members as well.

I have seen people just go straight to aftermarket axles to begin with rather then even bothering with the junkyards.