Try the following:
$find = '/jsfile\.js\?(version=)?[0-9]*</';
? makes the preceding element optional, and parentheses create a group, so (version=)? means "optionally match version=". Note that I also escaped the ? from earlier in the regular expression, since you want this to match a literal ? and not make the s optional.
In addition, I switched from double to single quotes to ensure the escaping works properly, if you were to use double quotes you would want to escape each backslash, for example:
$find = "/jsfile\\.js\\?(version=)?[0-9]*</";