You have a larger project than just that PanelView 1000E, so let's address those items one at a time.
PCE Errors are markers that the Translation Tool puts into the program to draw your attention to things it can't do automatically.
Timers are one of those things. The Translation Tool does the easy part of converting the Preset value from 1 Second or 1/100 Second units to milliseconds, but it doesn't know where else in the program or in the HMI application you might be using the .ACC or .PRE elements, so it flags the Timer instructions with a PCE to remind you to search those out.
The same deal with Status files; the same things don't exist (or function differently) in ControlLogix, so the Translation Tool flags them to remind you that you need to handle them yourself.
The I/O translation takes quite a bit of work, too.
There's really no easy or automatic way to convert a PLC-5C15 Scanlist into an RSLogix 5000 I/O tree. You just have to decide how much you're going to convert (do you need to stick with "N10[x]" as a data table format ?) and just go do it one at a time.
If you're willing to post the *.RSP, *.XC, and *.ACD files, I'd be willing to show you an explicit example of how to convert a PLC-5C15 connection to FLEX into a ControlLogix connection. Or you can chug along yourself, using the Knowledgebase or User Manuals, or you can recruit local help.