First, you're going to want to make a correction to the WHERE clause on your current query. As you've currently got it set up:
Where
(tblSoftwareUni.softwareName Like '%software name%' And tblSoftware.softwareVersion < 'software version%' And tblSoftware.softwareVersion Not Like 'software version%')
Or (tblSoftwareUni.softwareName Like '%softwarename%')
Or (tblSoftwareUni.softwareName Like 'softwarename' And tblSoftware.softwareVersion < 'software version%' And tblSoftware.softwareVersion Not Like 'softwareversion%')
Or (tblSoftwareUni.softwareName Like 'softwarename%' And tblSoftware.softwareVersion < '1softwareversion And tblSoftware.softwareVersion Not Like 'softwareversion')
Or (tblSoftwareUni.softwareName Like 'softwarename%' And tblSoftware.softwareVersion < 'software version And tblSoftware.softwareVersion Not Like '5.5.0.14558')
Or (tblSoftwareUni.softwareName Like 'softwarename%' And tblSoftware.softwareVersion < '10.13.0.0' And tblSoftware.softwareVersion Not Like '10.13.0.0')
Or (tblSoftwareUni.softwareName Like 'softwarename%' And tblSoftware.softwareVersion Not Like 'software version' And tblSoftware.softwareVersion < 'software version')
Or (tblSoftwareUni.softwareName Like 'softwarename%' And tblSoftware.softwareVersion Not Like 'software version' And tblSoftware.softwareVersion < 'software version')
Or (tblSoftwareUni.softwareName Like 'softwarename%' And tblSoftware.softwareVersion < 'software version' And tblSoftware.softwareVersion Not Like 'software version')
Or (tblSoftwareUni.softwareName Like '%softwarename%' And tblSoftware.softwareVersion < 'softwareversion' And tblSoftware.softwareVersion Not Like 'software version')
Or (tblSoftwareUni.softwareName Like '%softwarename%' And tblSoftware.softwareVersion < 'softwareversion' And tblSoftware.softwareVersion Not Like 'softwareversoin')
Or (tblSoftwareUni.softwareName Like '%softwarename%' And tblSoftware.softwareVersion < 'softwareversion' And tblSoftware.softwareVersion Not Like 'softwareversion')
Or (tblSoftwareUni.softwareName Like '%softwarename%' And tblSoftware.softwareVersion < 'softwareversion' And tblSoftware.softwareVersion Not Like 'softwareversion')
Or (tblSoftwareUni.softwareName Like '%nuance vmware%' And tblSoftware.softwareVersion < 'softwareversion' And tblSoftware.softwareVersion Not Like 'softwareversion)
Or (tblSoftwareUni.softwareName Like '%softwarename%' And tblSoftware.softwareVersion < 'softwareversion' And tblSoftware.softwareVersion Not Like 'softwareversion')
Or (tblSoftwareUni.softwareName Like '%softwarename%' And tblSoftware.softwareVersion < 'softwareversion' And tblSoftware.softwareVersion Not Like 'softwareversion')
Or (tblSoftwareUni.softwareName Like 'softwarename' And tsysAssetTypes.AssetTypename = 'Windows' And tblAssetCustom.State = 1)
Correction:
Where
( (tblSoftwareUni.softwareName Like '%software name%' And tblSoftware.softwareVersion < 'software version%' And tblSoftware.softwareVersion Not Like 'software version%')
Or (tblSoftwareUni.softwareName Like '%softwarename%')
Or (tblSoftwareUni.softwareName Like 'softwarename' And tblSoftware.softwareVersion < 'software version%' And tblSoftware.softwareVersion Not Like 'softwareversion%')
Or (tblSoftwareUni.softwareName Like 'softwarename%' And tblSoftware.softwareVersion < '1softwareversion And tblSoftware.softwareVersion Not Like 'softwareversion')
Or (tblSoftwareUni.softwareName Like 'softwarename%' And tblSoftware.softwareVersion < 'software version And tblSoftware.softwareVersion Not Like '5.5.0.14558')
Or (tblSoftwareUni.softwareName Like 'softwarename%' And tblSoftware.softwareVersion < '10.13.0.0' And tblSoftware.softwareVersion Not Like '10.13.0.0')
Or (tblSoftwareUni.softwareName Like 'softwarename%' And tblSoftware.softwareVersion Not Like 'software version' And tblSoftware.softwareVersion < 'software version')
Or (tblSoftwareUni.softwareName Like 'softwarename%' And tblSoftware.softwareVersion Not Like 'software version' And tblSoftware.softwareVersion < 'software version')
Or (tblSoftwareUni.softwareName Like 'softwarename%' And tblSoftware.softwareVersion < 'software version' And tblSoftware.softwareVersion Not Like 'software version')
Or (tblSoftwareUni.softwareName Like '%softwarename%' And tblSoftware.softwareVersion < 'softwareversion' And tblSoftware.softwareVersion Not Like 'software version')
Or (tblSoftwareUni.softwareName Like '%softwarename%' And tblSoftware.softwareVersion < 'softwareversion' And tblSoftware.softwareVersion Not Like 'softwareversoin')
Or (tblSoftwareUni.softwareName Like '%softwarename%' And tblSoftware.softwareVersion < 'softwareversion' And tblSoftware.softwareVersion Not Like 'softwareversion')
Or (tblSoftwareUni.softwareName Like '%softwarename%' And tblSoftware.softwareVersion < 'softwareversion' And tblSoftware.softwareVersion Not Like 'softwareversion')
Or (tblSoftwareUni.softwareName Like '%nuance vmware%' And tblSoftware.softwareVersion < 'softwareversion' And tblSoftware.softwareVersion Not Like 'softwareversion)
Or (tblSoftwareUni.softwareName Like '%softwarename%' And tblSoftware.softwareVersion < 'softwareversion' And tblSoftware.softwareVersion Not Like 'softwareversion')
Or (tblSoftwareUni.softwareName Like '%softwarename%' And tblSoftware.softwareVersion < 'softwareversion' And tblSoftware.softwareVersion Not Like 'softwareversion')
Or (tblSoftwareUni.softwareName Like 'softwarename')
)
And tsysAssetTypes.AssetTypename = 'Windows'
And tblAssetCustom.State = 1
Note the difference in the last few lines.
As to the files scanned, would doing a UNION of your current query with a query to identify your specific files do what you're after?
<your existing query>
UNION ALL
Select
tblAssets.AssetID,
tblAssets.Domain,
tblAssets.AssetName,
tblFileVersions.FilePathFull,
tblFileVersions.FileVersion,
NULL AS InstallDate,
tblAssets.Lastseen,
tblAssets.LastActiveScan,
tblAssets.Username,
tblAssets.IPAddress
From
tblAssets
Inner Join tblAssetCustom On tblAssets.AssetID = tblAssetCustom.AssetID
Inner Join tsysAssetTypes On tsysAssetTypes.AssetType = tblAssets.Assettype
Inner Join tblFileVersions On tblFileVersions.AssetID = tblAssets.AssetID
WHERE
tblFileVersions.Found = 1
AND tblFileVersions.FilePathFull LIKE '%pathname\filename%'
And tsysAssetTypes.AssetTypename = 'Windows'
And tblAssetCustom.State = 1