If you want to change trustees in Colorado, you do not need a new deed, just amend the land trust and file a new statement of authority with the County Clerk and Recorder.

Or should I just start with the straight 39 year schedule for everything (since it won't matter for this year) and then amend when I finally do the study?

If you've been claiming depreciation incorrectly for several years, you have a couple of choices.If it's been less than 3 years, you can amend your tax returns to claim the additional depreciation and you'll still get whatever benefits you may or may not have coming to you based on the lowering of your income.orYou can work through and file form 3115 which would allow you to declare this as a change in accounting procedure/method, correct several years worth of that change all at once and then move forward with the new procedure/method.  

Check to see if your local real estate board has any promulgated amendments available for this that you can use. 

However, I had to file an amendment for my 2016 taxes, and while doing so, the representative (at H&R Block) told me that since i rented out even part of my property, I do not qualify for this exemption.

I formed a single person LLC, but I've realized I should have formed it under my wife as she will be main person operating.I was about to start the process to file an amendment to remove myself from the articles of organization and add her as the sole member.But I read in Florida there are cases where the corporate veil can be pierced. 

You could amend and claim refunds of erroneous prior taxes paid but if you filed with the intention of misleading your lender you are likely committing mortgage fraud. 

Amend the lease, raise the rent.

Can I convert after purchasing  amendment to the lease and change it to NNN lease?

If you're willing to give them an extension make sure you amend the contract and put the new date in writing.