Toyota Repair: Engine Replacement problems?, noise problem, exhaust manifold

Question
I have a 1994 Toyota Extended Cab 2WD

Vin# T4RN93P6R5106359

About a year ago I had the engine replaced with a rebuilt engine. After the engine replacement I notice the Truck sounded a lot louder than normal...almost as if the muffler had a whole in it. I took the vehicle back to the shop I had the replacement work done and asked them to look into it. They told me that they didn't hear anything out of the ordinary and but did adjust the engine in some way that should make it quieter. I returned to them three other times through the year for similar issue (load sounding engine) but they insisted nothing was wrong.

Just last week I had an oil change and some brake work done on the truck (by another shop) and I asked them to look into the noise problem. They informed there appears to be a gap (opening) where exhaust manifold attaches to the engine. They also informed me that me that they didn't attempt to fix it because it looks like the bottom two bolts (where the gap is) that connects the Exhaust manifold to the engine are cross threaded and could break if tightened and/or loosened.

After I received this information I called the shop that replaced my engine and asked them what they thought. At first they wanted to blame it on a exhaust system replacement I had done about the same time but when I informed them that that work was done two months prior to their shops work they proceeded to tell me they didn't remover those bolts when they replaced the engine. They told me that there was a set of eight bolts they removed instead to get the engine disconnected from the exhaust manifold.

My question is this....

Can an engine replacement be done without removing the four bolts in question? I have been told that they are trying to pull the wool over my eyes, that there is no way to pull the engine in my care without removing those four bolts (two of which are now cross threaded)  but I am not sure.

Any help would be appreciated

Thanks


Answer
I'll try to answer your question the best I can, from the vin# I can tell that this is a four cylinder engine and I can tell you that the exhaust manifold has to be removed from the cylinder head to remove the engine and replace it. If the threads on the cylinder head are stripped out I would say it's their problem not yours.