Hi FL at CC,
I had the same problem with my 504, I ended up using old pennies and shilling coins as shims! You could check the lens panel and the negative stage are parallel and that the negative carrier is holding the negative flat.
The 504 head *and* negative stage can be independently tilted, so check they are correctly aligned. The movements should 'click-stop' when centralised.
You didn't say which head you have. If you're using an incandescent light source, the heat can cause negatives to 'pop', which can de-focus the image projected onto the baseboard. Medium and large-format negs are worse than smaller formats. If you have the Cathomag head or use an LED source you can ignore this.
If you don't have a focus-finder, consider buying one. It will save you paper and time (and hair!) in the long run.
That's all I can think of for now. I've attached two versions of the 504 manual. One is "new" and the other is "complete". Take you pick.
I hope you find it useful.
Good luck and happy printing,
kevs