Far be it from me to discourage any sort of performance upgrade. That said, I often find it useful to take a few steps back look at the big picture. The 400F is, stock, a really well thought out and very friendly handling bike. Keep this in mind! There is no question that you can get more out of it, but it comes with a price, and sometimes it pays to think a bit conservatively to keep your drive for performance from spiraling out of control. Suspension upgrades? great idea. Geometry changes? My opinion is that a little goes a long way. You can steepen up the rake for example, which will have (depending on who you ask) potentially good consequences. But it WILL come with a price. This is where attempting to brace the frame (this is so far away from amateur hour I don't have a description) to enable good use of the steeper geometry becomes relevant. My opinion is this: If you didn't ride around on you bike and after doing so said to yourself "gee, it really needs more ____ or less___, so I ought to change ____ to make it drive more like what I want", why in the world would you want to alter the geometry? More modern bikes have much steeper geometry than your old 400, but the makers have very massively strengthened the chassis to absorb the problems that arise from doing so. It will be quite a project to paste some reinforcement on the old 400 frame to bring it's natural frequency into line with modern geometry, but even if you could, is it really a benefit? Will you actually realize the benefit driving it around? You have made some very comprehensive changes already. I would make every effort to make an initial setup as close to stock geometry as possible. The short offset you have will add some trail, but you can always take some rake away to compensate if you think it too lazy. Set it up as close to stock as you can, start driving it around, and sort out the suspension. With the changes you have made, that will take some doing even if you are well experienced at doing so. THEN make changes to fix what you don't like about the way it drives. By the way, FWIW, I have a '75 400F and am pretty familiar with them. Used to race against them long ago, and I can tell you that in the right hands they work very well indeed stock!
You will have to excuse me now, I have to go change the spark plug in my lawn mower.