404 resolved page upon search but pages & sites do exist?

Hello all, recently I found malware on my site, after going through my files, I've found the malware, deleted it, and cleaned up other php in some other pages. However, I now have issues. Mostly likely with my htaccess file, at least from what I get back from google.

1. when i do a search for one of my sited on google, say newhopeqc.org i get a 404 error i.e.

but it searches like this...

how can I correct this. i'm told it's a htaccess file error, but unsure how to correct it.

2. however, when i enter the direct url of one of my sites it resolves to the correct site

Can you help me with this related issue?

Your help is greatly appreciated...

Thank You,

Adrian