Half Life 1 Modeling

Ok so I'm working on a map for team fortress classic, and needed a specific model, I tried making the models myself, that isn't the problem, it's when I try to compile them where things get interesting... I make my qc file, have all the model files, and compile it with milkshape (trial is over but it still allows me to compile qc files) it gives me the .mdl file, I load it into my map and the model is completely off center and the model seems to be broken into a few different pieces.

I figured I was probably making it wrong since I don't have much experience with modeling, so I checked the half life files, and they actually had a model of what I was trying to make, only it was the wrong color. So I decompile it, change the color of the texture, and since I don't want it to move, I removed the sequences on it so it would be still, and I compile. I load up the map and this time the entire model is together, only its about 100~ units above where it's supposed to be. Also, the only movement the model has is it spins, AFAIK, it never changes height.

Can anyone think of what I'm doing wrong? I've been looking on the web for around a week for guides for HL1 model editing, and nothing shows up, it's all for HL2 (which my models work fine in btw..) So if anyone could possibly point me in the direction of a -HL1- model editing guide, or can tell me if there is anything I should be doing that I might not be, it would be a big help.

thanks!