Well, I just recently finished the voicebank for my UTAUloid, and when UTAU was done processing the sounds, it was VERY choppy, and the sounds were much shorter than they were when I originally recorded them. (Recording Software suggestions appreciated as well!)

Would you guys have any advice on how I can make them work better?

Fixed it. Thanks for the help, guys!

Well, what program did you use?

It sounds to me a problem with a not configured oto.ini or the problem with resampler.exe and the decimal symbol being a comma.

oto.ini is a file that tells UTAU how to use properly the samples of your voicebank.
Let's say if your voicebank is a car, having no oto.ini is like that car using square wheels.
Check this thread or this tutorial for a starting guide on how to do it.

If oto.ini is not your problem and the problem appears even for other voicebanks with a good oto configured (you could check another one) it could be a problem with your resampler.exe not working properly.
The fix for that before was to change to resampler.dll and fight against how bad it renders some notes but it seems it was found a way to fix resampler.exe for those problems. Check this thread for more info.

About programs to record your samples, if you want to re-record again... the classical options are Audacity or OREMO. Recently Reaper is getting some popularity, too.
There are tutorials for OREMO and Reaper in youtube. I can't find any for Audacity but we have here one in "Tutorial and Resources Directory". Just dig a bit there.
But to tell the truth any program may be good to save the samples. Even Microsoft sound recorder could do it, I guess.

oh yeah this once happened on Kira's Beta VB...well the first VB he had. It's the oto.ini indeed.