It would probably be a good idea to use lock washers
on the bolts, which might give you the needed length.
If not, combine the lock washer with a flat washer.
Also, you can always measure how much room you have.
And maybe a drop of Loctite on the threads will help
to keep things together so you don't have this problem
again. Not too much though, as you will probably want
to take this apart someday.

Thanks. I appreciate the help.

Any idea why the bolts wouldn't fit?

I'm not sure which bolts you're talking about but here's the deal on the muffler cover bolts. There's not much clearance between the blade and the bolt heads, so you can't shim them out. I'm surprised you didn't have to replace the muffler plate. When the bolts back out, they usually start getting hit by the blade, which wallows out the bolt holes in the muffler plate. The new plate comes with non-threaded holes for the 'Tri-Round' thread-forming bolts. You should be able to use the original bolts.
The engine mount bolts go in from the deck side and you will see the end of the bolts. There are also several bolts holding the muffler plate to the engine - you access these below the baffle.

Saxman1-

You are describing the exact problem that he was having whe the muffler plate bolts came loose.

I am looking at the replacemnt muffler plate and it has non-threaded holes, however they do not go all the way through. When I insert the bolts with they break through the top side? On the parts diagram it look like the holes go all the way through.

Also the new bolts come with lock loctite already on them so I really don't want to experiment and have to keep putting the bolts in and out.

I can post pictures or try to explain further if what I am saying is not clear enough. Thanks for you help and patients with an amatuer.

Went ahead and installed the new bolts from under the mower deck into the new muffler plate and they ended up coming out through the top of the muffler plate.

I hope that is how it is supposed to be, it didn't take any extra force for them to pop through. It does seem very secure now, I hope it lasts!!!!!

Many of these mowers with the 'V' engine basically vibrate all the fasteners loose. Also check the shroud base to engine bolts and screws. If the shroud base gets loose, starting torque twists/bends the 'legs' and they break off. I have had every problem one of these mowers can have, but it was still functional when I sold it. I guess I had it for 13 years or so. All you have to do is check all fasteners twice a year, but I didn't know to do that and a lot of bad things happened. I never had any machine before that where it self-destructed in that manner.