...as it is warming up both the 5 volts reference 1 and 2 stay at 5 volts but once warmed up and when it runs ruff they are both highlighted in red 5 volt 1 now reads 5.01 and in read and 5 volt reference 2 reads 5.03 volts in red...
Which scan tool were you using when you saw this on the scan data?
Asking because Autel and Launch especially like to provide 'min-max' values for data PIDs. I really like the idea of providing a reference range, even when the OEM doesn't. But their provided values aren't always accurate, or realistic.

You have to take them as suggestions rather than rules.
In the case of your 5V reference PID, I think 5.01V or 5.03V is entirely acceptable and not related to why the engine is running poorly. 5.03V is still a pretty solid 5V. The sensors that use that reference aren't going to malfunction over .03V.
...also temp reads 220 + once hot they both high light in read, I would think it's a sensor but I just have never seen this before any pointers would be appreciated, also the motor was just put in to a used engine.
If it's got a used engine in it, then everything is suspect. :silly: I'd say put the 5V thing aside for now and keep an eye on your high level indicators during a warmup. Fuel trims, O2's, high and low side fuel pressure (desired/actual), coolant temperature, cooling fan control, and misfire counts. Does the fan ever come on? Do you get hot air at the dash vents?