Okay, this is my first post on this site even though I've been reading posts from here for a long time now.

I have a 95 Geo Tracker LSI 2 dr Hardtop 16v

Modifications:

Seriously cut fenders, Massaged fender wells, I had 31's now I have 235/75 Dueler AT's

I got rid of all the bends in the intake and have a cheap cone filter hanging behind the drivers headlight,
Original Exhaust Manifold going into a 2 1/4" pipe, magnaflow cat, and OEM type muffler for some added backpressure.

I did all the performance mods AFTER I mounted the 31's
Now, the issues.

Even with the 235's there is some serious bogging in 1st and 2nd if I'm below 3K RPM.

Once I get into the higher gears, riding at 2500+ RPM it drives great and I can hit 80mpg easy... but my low end is crap

Any Ideas?

Check your ignition timing, you might also have a bad cam timing belt that
has slipped and is causing the low RPM doggyness 

Wild

I forgot to mention it is a Manual Tranny, and I've already replaced plugs (gapped to .30), wires, cap and rotor.  Good fluids all around.

I have noticed a slight ticking sound on acceleration, I'm thinking it might be a small valve lash issue, but very small very quiet, and it's consistent between 800RPM clear to 5K.

As far as Timing Belt, I hadn't thought to check it, Previous owner didn't realize that a messed up locking hub makes a horrible noise that makes you think everything is going wrong.  So, I bought this at a great price only a couple months after he paid a shop to put a new belt in. (at 94K miles, I currently have it at 112K miles)

sound timing related to me and/or too low of grade gas. if it has done this the whole time you have owned it I would suspect the shop that did the t-belt job didn't get 'ER back in time

It had the smaller tires, and it's been a while, but I'm pretty sure it didn't do this until later.  I'm gonna see if I can't check the timing tomorrow.... err today.

As far as gas... It's not bad gas, I only go to frequently used pumps (costco etc) and rarely let get below 1/4 to 1/2 tank (things I learned while living in Alaska)

As far as low grade - I've had regular to premium in this thing, can't say I've seen a difference - then again I haven't paid too much attention with all the mods going on