Clicking noise?

Ok, this is one of the many problems im trying to sort out with my blazer
first of all, it is a '95 S10 LS...
I am hearing a clicking noise whenever I put it in gear, and sometimes in park or neutral and it gets louder when i give it gas, I am affraid it may be the flywheel but I just put a new engine in it and we inspected the flywheel and marked it for balancing before we did anything, I guess it could have cracked putting it in but it's highly doubtful, the noise seems to be comming from between the passenger and driver seat but more towards the firewall, I was underneath looking and noticed I have a leak where the driveshaft connects to the U joint, so that may be it also but I think I would be able to hear that from the outside of the vehicle but I dont.  we torqued all the bolts according to specs... does anyone know or have any ideas what could be causing this?

My first guess would be a universal joint on the front shaft.

hmm, I think you might be right, I was lookging through the haynes repair manual and it says U-joints will make a grinding noise when they wear out, I have to replace the seal anyway so I will raise it up tomorrow and take a closer look, when we swapped the engine we left the tranny raised up with a jack for a day and when we came back we saw that the jack had lowered so it might have messed up the bearings... more than likely

I had a broken flex plate in my old '85 S10 that sounded just like that before it fully went.

When you put the new engine in, did you make sure that both bell housing mating surfaces were clean?  A bit of misalignment in the mating surfaces can ruin a flex plate in a short order.

I got in the blazer this morning and noticed the noise had gotten way worse, I put my phone up to the floor where its coming from and recorded this...

http://s42.photobucket.com/albums/e346/iraqveteran/?action=view&current=04-07-08_1330.flv

I just listened to your video......a few times.
If you have a stethescope you should have a listen at various places to narrow down where it's coming from.
If you don't have a stethescope you can use a long screwdriver, put the point of the screwdriver on the trans or the engine and the other end against your ear.
Check that you don't have your accellerator cable or cruise cable resting on the PCV hose also.

Ok, I used the screwdriver method... nifty trick by the way, since I can only hear it clear from the top and barely at the bottom, Im thinking the torque converter bolts might be loose... but Im also thinking that 40 bucks an hour doesnt seem to bad to let a mechanic figure it out lol... I don't wanna go through all that work and find out its the flywheel, I can change a flywheel but I dont know how to balance it.

That wood pecker type sound is exactly what I had in my old S10 with a broken flex plate...  You can check to make sure that the bolts are tight to the torque converter though first.

A new flex plate will already be balanced.  IIRC, it wasn't that expensive...

ok, to check the bolts do I just have to take the bottom bellhousing off and reach my hand up there?  Also, can I use the flywheel that came with the new engine I bought or do I have to buy a new one that is balanced?  and how much did yours cost? flex plate is the fly wheel right?

Is the new engine the same as yours?  If so, then you should be able to use the flexplate (that's what it is called on an automatic trans vehicle).  They all should be balanced.

I finally got the chance to really look at the flex plate and there was nothing wrong with it at all, I even started it with the cover off and heard nothing... it has now gotten loud enough that you can hear it when you open the hood...
I drained the oil the other day into a clear tub and saw no metal shavings or anything...
it's not the U joint because it makes the noise in park or any gear.  Im thinking it could be a rod or something to that effect... any ideas?
Also, I bought this engine Feb. 15 of this year and started hearing the noise less than a week after installing it, so if it is the engine would I be able to get a refund on warranty from the salvage yard, I noticed the noise before the warranty was up but just didnt know what it was.

I listened to the video as well and the only that hasnt been mentioned is that it could be a bad PCV valve that is rattling like crazy or an accelerator cable resting on the PCV hose. Those are my guesses. You can view this by looking to make sure nothing is touching the PCV hose, also if you touch the PCV valve while the engine is running it should not be vibrating constantly, mine has been doing this since I replaced it so I am going to replace it again (after having taken one back to the store already). Good luck getting your problem fixed.