The rubber part you're referring to is the squared off O ring used where the ISCV's housing mounts to the upper intake plenum?
Part number:
90210-26001
http://www.cygnusx1.net/Supra/Librar...spx?F=2211&P=2
I could see how someone may have put it on an N/A engine if using gaskets from a universal kit... It would of course split from being crushed as the N/A's opening isn't as deep. It's quite possible and I can think of nowhere else for such a piece of rubber to have come from upstream.
You can't set the timing if ANY codes are present. If you set the timing after any of that previous work (or neglected to do so any time after removing the timing belt or distributor) then you should do so before mucking about with anything else.
The connector on your oil pressure sender is probably loose. It's located under the exhaust manifold and comes off sideways (not straight out). The sender is a metal can of sorts. Inspect the connector and the wire.
What VSV? There are three on the N/A. The TSRM covers how to test them.