Sorry for not being around today, but Sunday is not typically office hours. Support can generally only be expected Mon-Fri 9-5 ET.
"In-Place Upgrades," (1. upload files, 2. run upgrade script; nothing else) which is what it sounds like you had attempted,
were not possible until Beta 6 (and you had Beta 4). Even if you only needed to upgrade 1 or 2 versions, you still needed to disable the product before upgrading, per the instructions you were used to in Beta days. This was a serious design flaw in early versions (as you noticed), and that's why we fixed it almost a year ago in Beta 6.
To upgrade from versions before Beta 6, you MUST disable the product before uploading new product files, and you MUST NOT re-enable the product until the upgrade process has completed fully and successfully. You can only disable the product in the AdminCP, from Plugins & Products > Manage Products. Since you have run into errors, you probably need to set DISABLE_HOOKS in includes/config.php in order to even get back there.
Once the product is disabled, the errors will stop, and you should be able to run the upgrade script.
* You noted that Beta 4 is no longer available. As per our security and EOL policy, we remove versions that had security vulnerabilities (the most recent known vulnerability affected < 4.0.0 Gamma 3). We always email members whenever vulnerabilities are discovered, encouraging them to patch their installations at the time, since the exploit then becomes public knowledge.
I have made a change for RC 3 that will
attempt to allow In-Place Upgrades to work against pre-Beta 6 versions, but that does not help you now, and it would only work under specific circumstances anyway.