If both parties agree and sign off on the amendment to the lease is this ok?

Yes most of us get applications filled out, have a lease on computer so that it can be amended easily and do all of the work direct.

So here is what I am ending up with.  

I am pushing my agent to try and negotiate tomorrow and stipulate either that we negotiate those things now, or that we amend the contract that I still have a contingency after the inspection to negotiate these other issues without them being able to decline them since they are not in the inspection.this is my first purchase and I would be very thankful for advice on how to handle this situation before the contract becomes effective tomorrow. 

Also, I'm not entirely sure how this amendment will fix the constitutional problems identified in the cited cases.  

SeverabilityIf any court determines that any provision of this agreement is invalid or unenforceable, any invalidity or unenforceability will affect only that provision and will not make any other provision of this agreement invalid or unenforceable and such provision shall be modified, amended, or limited only to the extent necessary to render t valid and enforceable.10.

This way known issues are handled in the first version of the PSA and not future amendments.

I'm assuming since I did it wrong to begin with I'll probably also need to file a 1065X Amended Return?

There is no training or certification for a service animal/esa required under the Fair Housing Amendments Act of 1988. 

I am currently amending my leases for this as I just had an inherited tenant forget to put the drain hose from his portable washer into the tub and had been “sleeping” and ran the whole cycle while gallons and gallons of water flooded a downstairs unit.