Scott, I had a 1442 for a few years before I upgraded. In that time I changed out the bearings twice. The first was with Jet's shielded bearings and the second time around I went with the sealed type. The difference between the two, shielded have metal side walls, the sealed have a rubber compound. If they replaced them with the sealed type, you may find that they run warm for a while until they have broken in. This is common, however; if they are hot something may be out of alignment.
As for the spindle lock issue. With the spindle pushed in all the way, the spindle pulley should push up against the e clip that sits right behind it. This clip is found on the hand wheel side. There are only 2 spots in the pulley where the lock will engage. Check and see if the pulley is set in the right place, and then check if there are any breaks on the pulley itself where the lock pin goes in.
To check if the spindle is set, you can put a block of wood in front of the spindle shaft and tap with a mallet, or use a block of wood and bring your tail stock up and crank it in with the quill. To remove the spindle shaft you can spin the headstock around and use the quill as well.
The speed shifter is a tricky thing to get right. As for the shifter, it enters the front and then meshes with the short pole coming off the spindle pulley at the bottom. They probably did not match up the teeth at the end nearest the chuck side in the right position. When ever working on this lathe you want to have the speed set to the highest position. This includes when you put it back together. Having it in high allows for automatic alignment of the teeth.
Unfortunately, it looks like you or someone else is basically going to have to pretty much break it all back down again.
My in-laws are in holly springs, and normally I'd be up that way for Thanksgiving. This year they are heading down here. I'd be more than willing to come help if I was going to be up there.
The following is a write up from one of the guys, with pictures on how to do a belt and bearing change. I have one for the 1642 as well on that site.
http://www.woodturnersresource.com/extras/projects/pages/1442BeltBearing.html
I'll pm you my number, if you get stuck or need guidance feel free to call.