Did it have the original SD Card with it? If not what are you trying to use for a card? I have three of the Rep 1’s running here and i have fixed multiple others, and i can tell you they are very picky about the SD Card. It needs to be a plain old SD Card, and i mean old, not an SDHC or any of that newer stuff, and it has to be 2gb or smaller, it will not read a card over 2gb. The most reliable ones i have had are the same as the original that came with it. SanDisk white label 2gb SD Card. They are a Type 2 card, on SD Cards look for the little number in a circle on the label, most of the newer ones are Type 10, its the speed of the card, and you need the older card for it to work on the Rep1. Ebay is your friend unless you have a camera shop around, they generally have some older cards to keep older cameras going etc.
Buy Simplify3D, the Makerbot Desktop software stopped working correctly for the Rep 1 a long time ago, it just outright doesn’t work right anymore. At the bare minimum you will need to get firmware version 7.5 on the printer and then you can save to the SD Card from Makerbot Desktop, even the latest version, but its very buggy in the print results, sometimes it does ok, sometimes it misses pieces of the model, etc. I gave up on MBD about three years ago now, and went to Simplify3D, yes its not cheap, but you got a free printer!! Man why can’t i find things like that, busted and beaten ones go for $300 on eBay. The Rep1 is a solid older model, much better then their current printers, the 2 and 2x were good but had their issues as well. My Rep1’s are my workhorses, i have close to 6,000 hours on my first one, the second one is almost 3,000 hours and the third one is around 1,000 hours.
They are cheap to run, cheap to fix, and cheap to upgrade! Well worth the cost of Simplify3D, and trust me, its well worth the investment to get a good slicer like S3D unless you like wasting filament on failed prints!!
As for the USB issue… NEVER print from USB, its a nightmare. Any small computer background service can cause a failed print, the computer going to sleep, locking to the welcome screen, etc. I have seen many things crash the print. The last thing you want to worry about is the computer talking to the printer flawlessly for hours on a long print, use the SD Card thats what its there for.
As for the USB issue with Updating. Get ReplicatorG and do the update with it, but uninstall Makerbot Desktop or at least stop the Conveyor Service first. You can’t update with RepG with the Makerbot Software running, and yes even when you close it there is services for it running in the background. Safest bet is to uninstall it then reboot to clear them out and then try again. Also depending on your printer’s age it may not have got the later revision which added a capacitor for auto reset when updating, its labeled C20 on the Mightyboard near the USB port. It’s a .01uf ceramic cap that goes in that position, all the boards had the traces for it but not all of them were installed.
Last but not least, if trying RepG again after removing Makerbot Desktop still doesn’t work it could very well be a bad USB chip, its the AT8U2 near the USB port, i have replaced countless numbers of them over the years and they can and do fail. But all you really need it for is a firmware update cause as i said printing from USB is just plain pointless.
What version of firmware is on your printer now? When you turn it on it should show you the version number on the screen.
Edit… I see you said its version 5.1… Oh yeah your VERY VERY out of date. Version 7.5 is the latest version for the Rep1, and version 5.1 will not work with any version of Makerbot Desktop, that only works with the ancient Makerware that isn’t really archived anywhere anymore. I would guess you need something as old as version 3, i think there was a later version 4 and 5, those won’t work with your firmware as is.