I have not hit the ACL limits in a SharePoint list but I have seen posts that indicate the limit is 1500-2000 ACL items.  The OS limits an ACL to 64k. This limit can show up during indexing.

The simple solution is to use groups to control permissions for sites with more than 1000 or so users.

Read more: http://blogs.msdn.com/mattlind/archive/2007/11/02/sharepoint-indexing-limited-by-64-kb-acl-limit.aspx

I often see questions about redundancy in SharePoint index servers.

Couple of points to keep in mind:

• only one index server per SSP

• outage of index server will not cause a disruption in usage (unless the index server is also the a query server)

• a change to the index server requires central admin change (no automatic failover)

A SharePoint aware backup of the Index file and SSP search database will allow you to quickly restore a lost index server.

At crawl time document ACLs are stored.  If you add users to MOSS individually a crawl is required for any updated ACLs to be reflected in the search results. I you add users to an existing AD group a new crawl is not required.

I see lots of questions about running Central Administration on 2 web front ends (wfe)s.  This is certainly a good idea to ensure availability by avoiding a single point of failure.

Here are a couple of good resources on the topic. 

http://forums.microsoft.com/Forums/ShowPost.aspx?PostID=2022953&SiteID=1

To only allow users to edit custom web part properties you should override GetToolParts() as follows:

public override ToolPart[] GetToolParts()
{  
ToolPart[] toolparts = new ToolPart[0]; //empty array    
//add your own tool parts here     
return toolparts;
}