[TexasSwift]

Based on your comments and those of the board, there is one potential low cost solution that hasn't been mentioned. It has happened to me on other cars. Have them add an additional engine to chassis ground strap and check the battery ground at the starter The battery ground was removed when they removed the transmission and if the connection is not clean and tight will give you no voltage to many electrical systems. If the engine block is not grounded to the chassis you will have no voltage to many systems.
I would, if they haven't,
1. Add an engine to chassis ground.
2. Remove and check the battery ground at the starter.
3. Check both battery cables at the battery.
A complete loss of power to multiple systems and the problem being intermittant does not sound like a starter, a starter relay, or a key switch. I think it is a grounding problem.
The fusible link is a very large wire and hard to make go bad. When mine blow it blew 10 fuses, 2 relays and damaged the ABS controller, the transmission ECU and main ECU. I don't think that would be your problem.