I've always been taught to make it right before I go and try to make it better, unless you can make it better while making it right.
I'll answer the easier question first. You may not like the results if you re-gear for 33's or 35's and keep running a smaller tire. You'll end up having much higher RPM's at highway cruising speed. (ie 30" tires and 4.88 gearing @ 70 mph will result in an engine rpm of about 3k)
You can play around with the numbers here
to see what it would actually be for your current tires. I would suggest collecting the gears and master rebuild kits, and waiting on the install until after you have the tires. Then, take a weekend and install the gears. Remember that you have to re-gear both the front and the back to the same ratio or you will have some issues with 4x4, and maybe even cause some issues (ie breakage).
TBH, rebuilding a transmission or re-gearing an axle are probably a bit above and beyond for a relative beginner. Though you can find at least one solid walk-through for re-gearing and probably a couple for rebuilding an ax-5 here on the forum.
Have you tried Synchromesh from Penzoil in your transmission? I had the same grind when I shifted into 2nd, and it instantly went away after I changed the fluid and filled the tranny up with Penzoil.
At first, I didn't like my four squirrels. Then I noticed a fuel, dare I say, economy of 10 MPG, and realized that I needed to address some things with the engine. Long story short, If given the engine some maintenance type attention, and its running much better now. I have a couple things left to do to it, which I hope will make a bigger difference, but even at this point, I am not sure I would notice a real lack of power on a closer to stock driveline.