You have not provided much information to work with when trying to think of a solution to your issue. Probably the first thing to try is create a new project and select "reset" as the option while telling the Zoom how you want to proceed, as opposed to "continue" which will carry over settings from previous project. Plugging a guitar or mic into a Zoom is OK but not fantastic, I've used R24's for many hours which are a very similar beast and concluded that pre-amping via a mixer or DI is a better way to go, a tube pre-amp does the job well. The only time I've ever experienced stuff skipping is when I set a point A&B for repeated playback of a section of a track and then, that only occurs the first play through on rare occasions prior to setting point B. I think I'm correct in assuming you have a high and low switch for a couple of inputs, have you tried that option for guitar and mic inputting?
With the Zoom on its initial default track settings, the sound you get should be pretty much unaltered from what the source would sound like through any other means of monitoring the instrument or mic output via a flat setting. Yes it is fine to record direct input with your guitar and mics but you will need to watch the gain very carefully as it's very easy to overcook a guitar input once you start thrashing the strings.
all the best
Tim
