wow. too much info.
not sure where to start now!
FIRST GET A MANUAL its more or less the same as the 250/400 models
1) those are a home made ignition modules in the tail. Quite cool looking but not very reliable hanging out like that easy to get moisture in there. they are probably contact triggered as you still have the contacts.
2) as to carbs, its the passage ways you need to clean and I don't mean a quick blow job.
more info here http://www.xs400.com/tech.php
3) the head steady on top of the engine looks fitted correctly
http://translate.googleusercontent.com/translate_c?depth=1&hl=en&prev=/search%3Fq%3Dhttp://xs400.net/wb/pages/technik-faq/motor.php%26safe%3Doff%26client%3Dfirefox-a%26hs%3DlLG%26rls%3Dorg.mozilla:en-US:official&rurl=translate.google.co.uk&sl=de&u=http://xs400.net/wb/pages/technik-faq/motor/obere-motorhalterung-bei-2a2-und-4g5.php&usg=ALkJrhhb0rbKJpDjB6lygjwPGNEWH-L06g
you cannot just change the cam cover, its line bored with the head with matching numbers on the back stamped on them. you can get it ally welded though fairly cheaply
4) try swapping the orange and grey wires to the HT coils, many peeps get it wrong and the firing order is then 180' out
you have the largest vintage M/C supply company in Holland CMSNL, has loads of spares.