Like Soulinsane said, tube amps are very simple devices, solder points are very large, components are few, the design is simple, and so on
The JCM 800 is a great amp to start modding.
Here's some pointers:
More gain & bass: Add a cathode bypass capacitor (or increase the one already present).
More gain (clipping really) & compression: Increase the plate load resistor.
Just more gain and less buzzy tone: Modify & fine-tune the voltage dividers between gain stages (will explain more throughly tomorrow, it's late here).
Tone shifting: Modify coupling capacitors (google it) to a larger value for a darker sound, smaller for brighter. Change the values in the tone stack for a drastic change in tone, higher value means lower frequency (for example, change the bass cap. from 22n to 220n for a massive increase in bass and low mids, used by ENGL for instance). http://www.duncanamps.com/tsc/index.html
is a great tool for tone stacks.
Google "marshall tone stack" to find out more.
More clarity: Muddiness is often caused by "too many" components, i.e. the designers have added tons of capacitance to "safe" the design so it won't crap out no matter how crappy it gets built and how much off standards it is (too much high freq. cut between stages to tame over-excessive buzziness is an example, it muds things up, they should rather have less gain and then less cut), they add huge amounts of gain in each stage but then cut tons off before next stage to keep it from overloading (adding small amounts of gain in each stage and fine-tuning is FAR superior to going all-out in each stage and then just chopping off a lot to not get "bad" distortion in the next tube (blocking distortion)), etc.
A nice and solid power supply gets you a long way - check that you have a diode rectifier and plenty of filtering, adding some more caps in parallel over the existing filter caps can help. There's more on this but i will get back to it.
Google all the things you don't understand, like "voltage divider", "plate load resistor", "cathode bypass resistor" etc. Check out the preamp section of amps you like, and observe the small differences (they are mostly VERY similar).
Here's a VERY nice article for the JCM 800: http://tone-lizard.com/Ultimate_JCM800.htm
Also, read the info material on www.aikenamps.com
and check out www.ax84.com
, esp. http://18.104.22.168/ax84/media/ax84_m35.pdf
- nice theory on tube amps.
Also maybe some general theory, like Ohm's law, Kirchoff's laws etc may be helpful..