I would find any pages that's have external links, and only 301 them, as there is no use 301'ing pages that have no external links, you can 301 any url you want, the language is not relevant.

What server are you on IIS(Microsoft) or Apache? For Apache then use .htaccess for iis use web.config

Me myself I would not be moving to WordPress, you will end up with many more crawling problems

I believe you are right, i think i have a site that is been hit, yet I cant see what couild be wrong.

Maybe i spoke too soon

Yes.

you don't need both sets of files.

before the request reaches your pages, it is intercepted by the webserver and checks for any 301 rules. if it finds one for that url it will redirect, even if neither of the files exist. this all happens early in the request life cycle.

But as I said before, make things easy for yourself, only 301 the pages that had external links

in windows on a IIS server it would be

<match url="^category/1$"><action type="Rewrite" url="category"></action></match>

i think in a htaccess file it would be sothing like

RewriteRule ="^/category/1$ http://www.domain.lt/category [R=301,L]

Yes that's correct, or even on the same hosting account

More then likely they are no follow, even if they are not they are very low quality links, more likely no value at all.

I would not waste my time.

Unless those subdomains for single page sites, may look spammy to google. you can put those pages in your own site, there is nothing to gain using subdomains

I believe this is your problem, this plugin for WordPress.

http://dev30.linksalpha.com/?p=8

Sorry missed the bit about blog.
obviously blog.domain.com should not 301 to www
it should point to the correct site, then all reports and google will sort themselves out.

so add one more step, test that blog does in fact resolve to the correct site