Should I download the and client to a different machine? I read somewhere that it can oberwtie existing bitcoin code or something like that...
Yes, don't download qt and abc on the same machine unless you use a partiton or something like that. After that, you have to download the whole Chain.
I just noted that coinomi support bip38, did you try to insert the encrypted key and then the pass in coinomi? I really can't understand why it isn't working, besides some bug