I pulled a large ClearCase program into RTC using the Importer and luckily did not run into this issue (however, Eclipse did change the line-ending format, which screwed up quite a few files.) The Importer gets around these issues I believe, I'm assuming your team dropped in the code and committed by-hand if this is the case.

You fixed .log and .orig the correct way, however, I believe you are getting snagged on the .class issue because RTC doesn't advertise it's "builtin" ignored types. By default RTC ignores directories named 'bin' and all files ending in '.class'. In order to pull these in you must create a .jazzignore file at the root of the component and set its core.ignore.recursive set to empty. (In Pending Changes, in the Component, you would right-click a resource and hit 'Ignore' to generate this file, then hand-modify it to meet your needs.) This will allow you to control these files.

Here is an example of such a .jazzignore:
core.ignore.recursive= \
    {*.class}

core.ignore= \
    {.project} \
    {bin} \
    {build} \
    {classes} \
    {stage}

Also remember that RTC added a per-project setting that overrides a user's MIME/encoding settings so you can retain end-of-line delimiters on import, albeit it came in RTC 4.0.5: https://jazz.net/downloads/rational-team-concert/releases/4.0.5?p=news#delimiter-pref