Hi Clair, welcome to the Forum!

2 part epoxy putty is what you'll want for sealing the skimmer leak. If you need any tips on applying it, let me know.

The pinholes are a more difficult fix. I must say I'm surprised that the leak detection company didn't patch them as the discovered them??? Doing multiple patches on the deep end floor requires SCUBA gear to do the job right. Unless you have SCUBA gear and the time to patch the pinholes, I'd start with the skimmer leak and see how much water you are loosing each day, if the pinholes make you loose minimal water, you might be best off letting them go for now.

I think your most optimal fix will be to drain the pool, get under the liner to remove the cause of the pinholes and patch the underside of the liner while you're under it. A 2 year old liner should be able to be drained and refilled without any issues. Again, if you have further questions for me on this, I try to get here every day and am more than willing to help you solve your problems.