Rande, PitStop Extreme is not cheap. But there isn't much that you can't do with it.
I encourage everyone to use the PDF/X standards when working with external and internal resources. All PDF/X really says is that you have met a certain number of minimum requirements. Such as fonts are embedded, you have defined a size of the job, you have prepared it for a certain printing condition, you haven't used certain image compression types. PDF/X-1a builds on those basic requirements and additionally says "no color management/ICC profiles" (it's been pre-converted), no RGB or LAB colors, transparency must be flattened, and a few other little details. PDF/X-4 however says that you can have ICC profiles, you can have RGB and you can have live transparency.
PDF/X-1a is great for "blind exchange" where someone who doesn't know anything about your environment, or you, can prepare a page and ensure that it will contain everything necessary to image. Since you don't know how someone will flatten the art you (as part of the PDF/X-1a standard) flatten the art for them. It's the lowest common denominator. You can pretty well assume that anyone who can print a PDF can print a PDF/X-1a.
PDF/X-4 is even better because it allows for things like optional content groups (analogous to layers), ICC profiles (so you can properly convert colors) and live transparency (so you can flatten it they way you need to). But PDF/X-4 also requires a bit of communication so that someone doesn't go and do something stupid. But again, being a standard someone receiving a PDF/X-4 file will have everything contained in the PDF (since it is a content container) to reproduce the job. But it will take a little extra effort on the printers part to ensure that their RIP can properly render a PDF/X-4. Once the printer is confident in their processes and processing then I'd switch over to PDF/X-4.
The PDF/X standards don't really say anything like "this is CMYK only" or "images must be 300 DPI". Companies or organizations add those requirements to PDF/X to suit their particular needs. There is no reason that you cannot have a PDF/X-1a:2003 for a black and white job to be printed on a Xerox Nuvera. Similarly there is no reason that you cannot have a PDF/X-1a:2003 file that contains 8 spot colors. Or a PDF/X-4:2008 that has no live transparency but does have optional content groups.
Groups like the Ghent Work Group have developed "PDF/X-Plus standards". Way back when there was the idea of "PDF/X-Plus" to suit specific vendors/manufactures requirements. But everyone had their own "X-Plus" flavors. The GWG brought a bit of sanity to the world of PDF/X-Plus by further refining the ISO standards into logical groups of specifications. For example, magazines generally don't run spot colors but CMYK only, they like to have images at 300 DPI. So they came up with a agreed "standard" for lack of a better term. Then they did the same thing for newspapers, web offset, etc. Each segment had their own particular needs so they developed a specification for each based on those needs. It wasn't just the GWG that came up with these additional requirements. The GWG developed them with vendors in those particular segments.
Really when you look at each vendors PDF requirements you will find that everyone is basically looking for the same things but with slight variations. The GWG consolidated all those various "personal standards" into something more flexible.
But... Having said all of that PDF/X does nothing to say that you cannot edit or manipulate a PDF. So I suspect that your PDF editing tools aren't up to snuff (or date possibly). PitStop Pro 9, Callas pdfToolbox 4.x and Acrobat 9 should allow you to make most all of the changes you would need to. And many more that you probably shouldn't do. PitStop Extreme is much more adept at manipulating PDF's (whether they are PDF/X or not) than PitStop is. But be prepared to pay for such power. There's limits to what PitStop can do at its price.