Firstly, I know almost nothing about bikes... I have a Trek 7300 which I bought second hand a few years ago. Not sure how much is original or if there is any upgrades.
I am having two issues with my bike currently. The first one is an annoying clicking sound that comes from my pedals. It was only on the right one at first but it seems to have started on the left. I am 90% sure it is the pedal making the noise because of the sound as well as the fact that I can feel it. My second problem is a a very inconsistent speed reading from my Cateye Enduro 2 computer. the speeds jump all over the place ranging from 9-46 km/h. It was fine up until I had to replace the battery in it. The magnet seems to be in the right spot and the cables and connectors all seem to be in order so I'm not really sure what else it could be. Thanks.

Possibly the easiest to check and fix cause for crank/bottom bracket/pedal creak or click is the pedal itself.

Remove one or both pedals, clean the mating faces on both the crank arm and pedal, check that the threads a re also clean (usually are) add some frsh frease and reassemble, tightening them tight, or somewhere in the 25 foot pound range. You don't need a torque wrench, just one about a foot long and press on it with 25#s of force, or until the pedal feels bottomed out, plus a bit.

If that doesn't solve the problem, try another set of pedals, which if that works means your pedals themselves were the problem, or if not, that it's elsewhere, like a loose crank arm, or bottom bracket issue. Note that clicking cranks are the hardest diagnostic on a bike, so if you're not luckly early on, you're facing a long frustrating job. Though the noise appears to be in the pedals or cranks, it can be anywhere and the list of causes discovered by others is a mile long and as far away as the wheels or fork.

As for the computer, sounds like a bad connection someplace, possibly happened when you replaced the battery.

It's uncommon to have a properly set computer display a faster speed then you're actually going. Slower speeds are the usual as the spoke mag fails to trigger the sensor or a single is lost due to cable shorting or head/shoe contacts being dirty. I'd first go back the battery install and pencil eraser off the battery contacts before closing the lid. Do the same for the underside of the head and the shoe contacts. Then recalibrate/reset the head. Take care to get the KPH/MPH right (there's a 1.6/.62 difference right there). Next most common bug is the wheel circumference being wrong. A true roll out measurement is best. It's real easy to mess up just one click during the calibration and set a really off result. While in use the biggie problem is the mag and sensor being poorly adjusted, but this is the easiest to check for and correct. Andy.

I was suffering from the clicking sound in a pedal also. Went through the removing pedals, greasing, etc. Still had the problem. Finally did a Google search as saw a recommendation on oiling contact points on my cleats with chain oil and letting sit over night. Tried it and worked for me.

Did you get the exact replacement battery?