Many Initial Issues - Please advise

I got two identical new MBP on Wed at the Apple store. I had Time Machine backups from two other older MBP that I used. I ran each of those on the new laptops. Since then, one has been perfect. The other has had many issues...
- Already one crash
- Insanely long start up times (currently trouble shooting this)
- The trackpad skips and freezes constantly
- The fans are nearly running at 100% all the time now. I think this has to do with start-up, but not sure.
I have run disk permission repair. I have clean cache files. I have run and cleaned out tons of other stuff, with no luck. SHortly, I'm going to do the P,R,Alt,Apple in just a min to see if that does anything.
Any other ideas? Anyone suggest I just take it back? I was told I have 3 days buyer's remorse with no fees and stuff. Is it possible I just have a lemon? I really do not want to spend the time on a clean install and testing for another day or two... that puts me over that 3 day limit, then I have to pay restocking fees, etc.

Thank you all for your insights. I stayed up until 6am last night (this morning) trouble shooting. After a few clean installs, restores, etc. I did a clean install, then restore, then an archive & install. That seems to have fixed the problem. The problems only manifested after my restore. But the last time I did an archive/install so all the system files are fresh and not from my TM restore. When using a TM backup, there is an option to not copy over your system/library files, unfortunately this option was checked and grayed out, so I didn't have the option NOT to install those files.
I do still have one whole day. I'm putting it through it's paces today, and if there's any problems at all, I will return it and hopefully just get a new one right there.
Thank you all again. If anyone has specific insight into why this happens, I would still like your input.

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