Powering several 12 V @ 1A Vacuum Pumps
How many is "several"?  You can operate three 1-amp loads from a 3.5A supply.  And if you are powering other circuit from the same supply, remember to factor those loads into the sum also.

Not clear whether you are saying that you want to operate ALL THREE loads on your TIP31. Clearly, the TIP31 is rated at 3A, which means that it can control three of these 1A loads combined.  And remember to use adequate heat-sink.

OTOH, using one transistor per load would be a much more conservative design.