Negotiate with the Seller: Depending on the market and the seller's flexibility, you might be able to negotiate a lower EMD or even delay the deposit until a later stage in the transaction.

Apologies for the delayed response!

You can also consider buying materials during off-season sales.Tight Project Management: Keep projects on schedule to avoid costly delays.

I would imagine I would still get the house inspected and appraised to minimize the risk.

As long as you are in your due diligence contingency you can back out with minimal expense.

Since our goal is to scale in real estate and we do have the funds, we would prefer to minimize the deposits and invest into reno where necessary and keep the capital for now for improvements, if they arise.

You want someone self-certified to avoid delay from multidepartment review (there's a list of maybe 700 of these architects on the City site).

He ended screwing me over big time with months of delays and going 20k over what was originally quoted.

The benefits of selling as a portfolio is that when you do a 1031 exchange, you won't have to coordinate the sales of multiple properties, And this would minimize the amount of individual exchange fees. 

Nothing wrong with trying to minimize your taxes.