New roof, new AC, moving electric panel (fortunately electrical had already been updated and house had been re-plumbed), new flooring throughout, new kitchen, new M bathroom, updating 2nd bath.

I bought a house and fully rehabbed it myself, learning everything from plumbing to electric and framing.

Well, since you can't rip the walls to look at framing, wiring, and plumbing, look at what you can see:1) Level of trim, appliances2) Finish carpentry or gaps in joints3) The flatness of floors and squareness of rooms. 

This will help you get a better idea of what tile, hardwood, carpet, plumbing fixtures and light fixtures costs for your rehabs.#3 Contact Local Contractors for Labor PricingCall local Subcontractors and get budget pricing for common repairs on your typical rehab project.For example, call a roofer and ask what their average cost per Square of Architectural Asphalt Shingle Roofing would be on a 1,500 sf house, with a 6/12 pitch.Note: Some contractors will be reluctant to share pricing without seeing the property, but tell them you are just looking for a rough budget number you can use on future projects.#4 Compile Your Prices into a Spreadsheet or a DatabaseOnce you start to get a better understanding of Labor and Material costs you will want to store this data in the spreadsheet.The House Flipping Spreadsheet has a database of common repairs & budget prices to help you get started, but you really need to start building your own cost database based upon your specific projects, materials & contractors in Chicago.#5 Practice, Practice, PracticeWalkthrough potential rehab properties (or find properties virtually online) and practice creating detailed scopes of work, quantifying repairs and estimating rehab costs for the projects.#6 Complete Your First Rehab Project It sounds like you are already half way through your first rehab? 

Watch out for plumbing or electrical that hasn't been updated. 

We rescinded an offer on a different property because it need new roof, new water heater, new furnace, new electrical wiring, there was some unknown plumbing back ups and leaks.The owner would not budge on the price.I just don't want to go forward with this other property and have some major expensive repairs going in the first year.

Needs new electrical service to home and plumbing throughout house.

I also have experience in hands on rehabbing myself, I've personally done electrical, plumbing, framing, sheetrock, paint, fabricating, landscaping, mechanical, carpet, flooring, roofing, demo, etc.

However, it turns out the property is now marked for plumbing, mechanical and electrical violations.

As far as plumbing, we just have an upstairs sink that tends to leak.