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,