You will need to trace the interest to either personal spending, investments or the property... and that tracing will determine the character (nondeductible personal, qualified mortgage indebtedness interest, investment interest, interest on production of income activity, etc).
E.g., the $250K you trace to the improvements? That'll be more rental property interest and so potentially deductible on Schedule E.
The $60K or whatever you trace to the HELOC? That'll be nondeductible interest, possibly, if you used the HELOC funds for personal spending. (Or did you use HELOC funds to buy home or income property?)
The remaining funds you use to invest in stock market? That interest will be investment interest expense and potentially deductible.
BTW, you should probably consider having a local tax accountant check your accounting given the dollars involved.
P.S. Whether the HELOC interest is deductible or not depends. I've got a long explanation of the mortgage interest deduction rules for 2018 here:
New Mortgage interest deduction rules