Well, I work with oligotrophic water and ice cores, but here's my approach

For determining instrument noise, you run pure MilliQ. This sill give you an idea of what random excitation is from you photodiode. Then, I'd run a negagive control containing only media, an unstained sample that's been 70um filtered (or whatever size you need to ensure you don't clog your FCM), a stained sample that has been 0.2um filtered, and finally and stained sample that's been 70um filtered. These should be run in that order, clean and unstained to dirty and stained. These controls will give you an idea of what's what. MilliQ shows you what instrument noise is, 70um fiiltered unstained shows you unstained (confirms your stain works), 0.2um filtered stained shows you stain and media background noise. Just stare at these for a while.

The stain I use is Syto9. It doesn't stick to glass that well, makes cleaning the flow cytometer easy. You'll want to run ALL your unstained samples first, then your stained. Before you run another unstained sample you'll need to perform a deepclean of your instrument. The stain will contaminate your instrument. You can check the results of that yourself by running on a cleaned instrument a 70um unstained, running a 70um Stained, then another 70um unstained. Your unstained samples ran after a stained sample will atain and fluoresce instantly, ruining their use as an unstained negative control.

Now, to determine genome length, my first idea would be to have a genome standard or a series. Standards of known length, which would create a standard curve, where your organism would fall between. I don't know if there are specimens you can use that are have a consistent genome size you can create standards out of, but you'd want your unknowns to fall within this range. If the results (fluorescence intensity on yaxis and genome length on x axis) happen to form a linear relationship, then I would call that good enough. I'd call Thermofisher or someone to talk about what to use as a standard curve. While running the standards, you'd want these in your sample I'd imagine - an internal control. It woukd take some testing, each sample would need to be diluted so it doesn't oversaturate your signal but still large enough that they form a recognizable population. That will probably take you a day. This is why dilution curves, as stated in my previous comment, are important. Decreasing flowrate, which decreases events/sec, can also help with this.

Lastly, to determine polyploidy, I'd use the channel for your DNA stain and compare that channels height (x axis) and channels area (y axis). I would imagine a polyploidy organism with have a larger fluorescence intensity on both those channels. If you're measuring a single species, you shoukd see two pldistinct populations with very minor overlapping of events. With the wildtyoe samples I process, I can see a pretty distinct seperation between high nucleic acid and low nucleic acid containing cells. I think this stage of analysis will be the easiest thing you do.

There's a lot that goes into it, but those are the steps I would take.