A: Rich,
All the files we found today - were dated; Apr 6, 13:58 server time (PST).
We did the restore for you on Apr 3rd; it's unclear if you were able to successfully get upgraded to vB 4.1.11 ; as you reported still having problems and missing files on Apr 7th.
So in the "how are they getting in" - I'm tempted to say - now that we know we have a fully cleaned - and fully patched vBulletin 4.1.11 - let's see how things go.
On the "fully cleaned" front - we also found this file was also modified; we reverted this back to the known working version you provided.
/forum/install/vbulletin-upgrade.js
Finally we found a small number of files that are present in your nyshooters.net/forum - directories that are not in the uploaded files you gave us.
Most of them make sense - the list is below.
However this one file ( which was also modified in the same way with encrypted data ); does not appear to belong in this location at all; we went ahead and deleted it.
/forum/includes/vbulletin-threadlist-ie.js
The real file appears to be located in:
/forum/clientscript/vbulletin-threadlist-ie.js
Each of the following files should be closely inspected; but we already did a file by file check - visual inspection of each file did not show any of the same style of encrypted data - that other hacked files included. ( since this hack uses a data encryption method - our normal Anti-Virus software does not find anything - which is why we need to visually "look at" each and every file ).
Anyway all of the following appear legit - but you may want to take a 2nd look just in case.
Only in ../nyshooters.net/forum/admincp: itrader_misc.php
Only in ../nyshooters.net/forum/images: graphics
Only in ../nyshooters.net/forum/images: itrader
Only in ../nyshooters.net/forum/includes: class_dm_itrader.php
Only in ../nyshooters.net/forum/includes: config.php
Only in ../nyshooters.net/forum/includes: functions_itrader.php
Only in ../nyshooters.net/forum/includes: functions_itrader_urlcheck.php
Only in ../nyshooters.net/forum/includes: itrader_detail.php
Only in ../nyshooters.net/forum/includes: itrader_feedback.php
Only in ../nyshooters.net/forum/includes: itrader_global.php
Only in ../nyshooters.net/forum/includes: itrader_main.php
Only in ../nyshooters.net/forum/includes: itrader.php
Only in ../nyshooters.net/forum/includes: itrader_report.php
Only in ../nyshooters.net/forum/includes/xml: bitfield_itrader.xml
Only in ../nyshooters.net/forum/includes/xml: cpnav_itrader.xml
Only in ../nyshooters.net/forum: itrader_detail.php
Only in ../nyshooters.net/forum: itrader_feedback.php
Only in ../nyshooters.net/forum: itrader_global.php
Only in ../nyshooters.net/forum: itrader_main.php
Only in ../nyshooters.net/forum: itrader.php
Only in ../nyshooters.net/forum: itrader_report.php
Everything else now matches the exact file/directory structures you uploaded to us - so your forum appears clean.
-Michael