Hi,
To start of I really like the changes you made, i'm a big fan of the original game and you made the game even better!
During the play though i found a few bugs and have a few ideas, maybe you can take a look at it
bugs:
1)If you hack a lan server and cancel you get a popup "you are currently accessing files" and are then kicked out of the system the program will crash and are not able to click on yes or no. A fatal error occurred popup did appear.
I used the Gold version 1.04 in combination with the GOG edition.
2)Protovision Game Server should not hackable, you need to know the password.
3)When connecting to some lans the last hop should be of the same company
4)When you delete files from the main server in a lan via the console and you get kicked out before it's completely finished , the deleted files are still there.
5) when you nuke your computer, and get into your account it looks like it is a new account and are connected to the uplink public server instead i did receive the email "Gateway seizure"
ideas:
6) request: if would be nice to include the FBI server a into UplinkOS
7) app idea: tracer for lans, so you know which hop on the lan the admin is. maybe an upgraded version can extend the time (especially usefull when modem is directly next to the server)
8) Taskmanager upgrade: normally you need more processing power for password cracking or decyphering. but when you max it out the applications like tracer or proxy are going into the red and are not functioning anymore.
it would be nice to have a button (maybe in task manager 3.0) to set it to the minimum required before so the applications you need still keep working and cannot go into the red.
9) in lans there are only a few passwords saved, it would be nice if the last known passwords are saved and not the first few. or just all of them 
10) in the jobs BBS if would be nice if you could filter on "Good" or "Bad" jobs so the destroy machines would be increasing your Neuromancer rating and trace a hacker would lower it.
