Well, I agree with pretty much everything said above. The best bang for your buck is the 466 kit. It will increase displacement by roughly 16% and increase the compression ratio about a point (IIRC). The next thing to do, which is actually the biggest choke point on your engine, is to increase the air flow through the carbs. Have Rick Denoon bore them out, and you'll be shocked at the power increase. Plus, you won't have to mess with your jets much if you stick with the stock airbox. I went with a 466 kit and bored carbs with the stock airbox and ended up leaving the same jets in, or possibly one size up on the mains. That stock intake will be fine for whatever you do too, unless you decide to go with velocity stacks, but it'll be a pain to tune.
After you make those two changes, you should consider your exhaust and a port job next since they will then be your limiting factors. Another tip is to take one coil off the advance springs and change the stock "fire" setting, but I'll defer to Hondaman about that since he's the one who discovered it.
If I were you, then I'd consider putting money into the suspension after you bore the cylinders and carbs. By the way, bored cylinders and carbs will effen shock you with the increase in power. It is VERY noticeable. So, suspension, get some decent rear shocks (hagons are totally fine, but get them for your weight and get the 13.1" bodies), send your swingarm to Hondaman for a rebuild, but put in tapered steering head bearings FIRST!!!! Replace your fork oil too with 10 weight fork oil that you can get at any motorcycle store.
After all that, your next step should be a billet lower triple tree since the stock one is a flexy pile of poop, and upgrade your front suspension. TTR400 makes a very nice aftermarket lower triple tree setup, and he is a super cool guy, so you'll be happy sending your business his way. FYI, I just bought two triple trees, various adjusters and a pile of other goodies off him.
Front suspension can be improved with new springs, pre-load adjusters and emulators, although I have ZERO experience with emulators so I'm just going on what others say.
So, there you have it. Power and suspension, but please keep it stock looking! I just love seeing those old stock 400s tearing along in the twisties. By the way, I've put my 350f through its paces, and I can tell you that keeping up with a GS500 should not be a problem on your 400. In fact, I'd be willing to bet you'll dust your sister since those 500s aren't exactly handling majis!
Good luck and report back with progress please!
Camelman