I'm sorry, I forgot to mention that I use FAR. It came recommended in the Basic Aircraft Design tutorial. What made sense to me was that KSP adds the drag from each component and not just those on the outside. The example given is a probe inside a fairing has more drag than just the probe on the rocket. This made sense to me. Does it not do this? (That guide was posted seven years ago but edited just before KSP 1.9.1 came out, but after 1.9, so I don't know what that means.) Other than that there's Mod Manager and Docking Port Alignment Indicator. (Sometimes I really wish this machine could play Orbiter. So much instrumentation, but no spacecraft construction!) I didn't initially auto strut the wings because I didn't want to poke the Kraken. I'm running on a laptop and KSP doesn't run at its best. I've read that excessive autostrutting could cause problems, and those wings have more parts than I'm comfortable with, that's why I went with the S-wings on the second version. I don't remember if I saved that one auto-strutted or not.
I'll try the fuel tank replacement, I hadn't thought of that, or measured my fuel, really. The airplane vertical tail made me nervous though, I'll replace it. So far all my r"e-entries" have been from the atmosphere anyway so it hasn't come up.
Edit: I tried your flight profile, and I think I just need to practice with it: I keep ending up rolled a little to one side or the other and attempts to correct it lead to more problems. But on one of my flights the Structural Wing Type B on both wingtips fell off and it flew just fine until it didn't. They move the CoL forward though so I'm going to leave them. And it doesn't seem to want to climb that fast. I've also added batteries and the RCS, so that's covered for now. (I didn't notice that rapiers don't have an alternator! I just sort of take it for granted. I need to find a solution to that...)
But thanks for your help! I'll keep practicing, and hopefully I'll get it well above 1Km.
-Jake