I have an MDD which was a single 1GHz FW800 with 768MB RAM and a 133MHz bus.

It still has the 133MHz bus, but is now a dual 1GHz with 1.75GB RAM and a DL burner.

I have added a USB2.0 card with an internal port, but I don't use the internal. Just needed 2.0 for my Nano. I do now have a plan for the internal, but I'll save that for another time.
I'll address your other points one by one:

1: You did this already.

2: The RAM limit is not something you can get around. Its a hardware limit imposed by the configurations of RAM modules the memory controller can address, and the number of RAM slots. The only way around it would be to replace the memory controller, add more slots, or build custom RAM modules. None of these are practical unless you know how to redesign a logic board or design RAM sticks. If you can do this, you can probably afford much faster kit to play with.

3: This is something I was interested in and cast feelers around for a while back. No-one could help me out with precise instructions, though I did find one guide from a slightly newer machine. I did't want to risk this sort of mod in case the parts used in the guide differed from my own. This mod is especially attractive to me for the following reasons:
There were a number of machines running a 167MHz bus before mine, so the chances are mine was downclocked from its true potential, and will run happily at 167MHz. (this is not necessarily so true of the CPUs).
Upclocking the bus not only boosts the bus. A faster bus means potentially faster access between CPU and drives or AGP/PCI cards. It should also upclock the RAM if the RAM is fast enough (most of mine is pc3200/400MHz or pc2700/333MHz, rather than the stock pc2100/167MHz). The CPU's clock speed is determined by multiplying the bus speed by a number which can be determined on the daughterboard (or in some machines the firmware). The number is called the multiplier. Since we are talking about the bus, you can see that my multiplier is 7.5. (7.5 x 133 = 1000) If I up the bus to 167MHz, my CPUs will jump to 1250MHz.
So a faster bus = faster CPU, RAM, drives, graphics, and other connectivity. Not bad if you can do it. Let me know how you get on if you try this. I forget the site I found, but it was australian if that helps.

4: If your bus is 133MHz, your mulitiplier is 6.5. If you clock up to 167MHz, you'll get 1085MHz. Shouldn't be a problem, especially if you add fans.

5: I'll leave fans to someone else, as I haven't bothered to play with mine aside from adding one to my graphics card. Others here know alot more about fans.
I mentioned USB cards. You can power something from the internal. USB is 5V and the pinouts are readily available online, so all you have to do is chop one end off a USB cable and wire it to whatever you want. Many fans will run on 5V.
Graphics cards are also probably best left to others, though I have fitted an nVidia GeForce FX5200 from a G5 to mine, and bolted a fan on it before overclocking it. See my mod guide if you want more about that.

Thats all the wisdom I have to pass on. Best of luck.