in terms of mileage, reliability, speed and engines go with a sidekick. to be straight on with 31s on a sidekick you may want to find some 5.62 axle gears  but the more common 5.12 will be fine.

First off, where do all you guys search for your sidekicks/samurais? I have been looking on craigslist but no one has good sidekicks or samurai
Craigslist, local off road forums, other local classifieds (both online and paper).  Ebay, if you want to pay a premium price for it.

Do these sidekicks drive better than the samurai in terms of mpg and speed?
Yes, the trackers and sidekicks (trackicks) drive better than the samurais, in my opinion.  The trackicks have larger, more powerful engines and will run faster than most samurais.  The MPG is comparable, between trackicks and samurais.  Although, usually the trackicks will get slightly better MPG (1 or 2 MPG better, in my experience).

What does it mean if it is a jx or jlx sidekick and what does the IFS mean!?
Those are trim options.  JX means it is a 4x4.  A JLX package adds power windows and locks and maybe a few other options.  There is also a JA....which means it is a 2wd.
The Sidekick Sport that was mentioned earlier, are the ones with the 1.8L engines.  They were only made from 96-98.  I would not buy one, mainly because there are lots of parts on it that are specific to it and used parts can be hard to find, since they were only made for 3 years.
IFS stands for Independent Front Suspension.  The trackicks have an A-arm front suspension with coil springs and struts.

If it is 16valve or 8valve what does this mean and what are the engines in terms of years for sidekicks/samurais? (EX: 80-92 samurai = 1.3l    (i dont know but you guys get the setup)
8V and 16V is in reference to how many valves are in the head of the engine.
89-93 2 door trackicks had the 1.6 8V engine with EFI (electronic fuel injection).  Some 2 door 89 sidekicks had a 1.3 carbed engine (but they are pretty rare to find).
94 2 door trackicks could have either the 1.6 8V engine or the 1.6 16V engine (if it was made for a NY or CA market).
Two door 95 trackicks that were 4x4 had a 1.6 16v engine.  Two door 95 trackicks that were 2wd had the 1.6 8V engine.
All 96-98 2 door trackicks had the 1.6 16V engine.
91 4 door trackicks had a 1.6 8V engine.
92-98 4 door trackicks had a 1.6 16V engine, except for the Sports that were made in 96-98, they got the 1.8 16V engine (regular trackicks were also made in 96-98 too).
From 99 and up there were some other engine choices...2.0, 2.5, 2.7 etc, in addition to the 1.6 16V.  But I am not familiar enough with the trackicks in those years to be able to tell you what engines were available in what years.

I would want to put a nice exhaust/header setup but when i searched up the forums i get confused so quickly as you choose sizes and ugh!!!
Most any name brand header should be ok.  Most run a 2" exhaust, when running a header.  Personally, I don't think a header and bigger exhaust is worth the cost.  If you are just going for sound, then knock yourself out.

What tire size is best to put on the sidekick anyways? i was aiming for nothing bigger than 31 as i dont want it to interfere with the gears or speed when i am driving and have to change the gears and then find that it says i am going 50 when i am going only 20mph...i know i would have to shave a lot on the fenders but how much exactly? and is 31x13.50 too much of a tire to put on it? is it better just 31x12.50?
Bigger tires will affect performance and MPG.  It will accelerate slower and the MPG will likely drop.  How much depends on how big of a tire you run and what type.

Which car would you guys choose in terms of speed, mileage, reliability, and engines?
I would take a trackick with a 1.6 16V over a samurai, if you are looking for mainly one to drive on the road.  If you are looking for one to off road, more than drive on the road, then the samurai is the better choice, in my opinion.

mpfi motor is with the 16 valve which means what (mpfi?) and 2" is the one i was aiming for although i also saw 2.75 so that was why i was wonderign what are those used for and benefits = what?

You will find that for each inch of width you will see a significant drop in mpg when you get up into the 31"+  tires, not too mention the rather large amount of fenderwell massaging that will be required.

I am running 31-10.5"s and they are borderline too wide without dropping another grand on 5.62 R&P's. With the rather ultra lightweight of the Suzuki's the 10.5's have plenty of flotation, and I can skitter along while the heeps and other large trucks sink to the frame+.